1
|
Zhu D, Cao D, Zhang X. Virus structures revealed by advanced cryoelectron microscopy methods. Structure 2023; 31:1348-1359. [PMID: 37797619 DOI: 10.1016/j.str.2023.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/25/2023] [Accepted: 09/11/2023] [Indexed: 10/07/2023]
Abstract
Before the resolution revolution, cryoelectron microscopy (cryo-EM) single-particle analysis (SPA) already achieved resolutions beyond 4 Å for certain icosahedral viruses, enabling ab initio atomic model building of these viruses. As the only samples that achieved such high resolution at that time, cryo-EM method development was closely intertwined with the improvement of reconstructions of symmetrical viruses. Viral morphology exhibits significant diversity, ranging from small to large, uniform to non-uniform, and from containing single symmetry to multiple symmetries. Furthermore, viruses undergo conformational changes during their life cycle. Several methods, such as asymmetric reconstruction, Ewald sphere correction, cryoelectron tomography (cryo-ET), and sub-tomogram averaging (STA), have been developed and applied to determine virus structures in vivo and in vitro. This review outlines current advanced cryo-EM methods for high-resolution structure determination of viruses and summarizes accomplishments obtained with these approaches. Moreover, persisting challenges in comprehending virus structures are discussed and we propose potential solutions.
Collapse
Affiliation(s)
- Dongjie Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Duanfang Cao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinzheng Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
2
|
Wang Z, Fokine A, Guo X, Jiang W, Rossmann MG, Kuhn RJ, Luo ZH, Klose T. Structure of Vibrio Phage XM1, a Simple Contractile DNA Injection Machine. Viruses 2023; 15:1673. [PMID: 37632015 PMCID: PMC10457771 DOI: 10.3390/v15081673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/26/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
Antibiotic resistance poses a growing risk to public health, requiring new tools to combat pathogenic bacteria. Contractile injection systems, including bacteriophage tails, pyocins, and bacterial type VI secretion systems, can efficiently penetrate cell envelopes and become potential antibacterial agents. Bacteriophage XM1 is a dsDNA virus belonging to the Myoviridae family and infecting Vibrio bacteria. The XM1 virion, made of 18 different proteins, consists of an icosahedral head and a contractile tail, terminated with a baseplate. Here, we report cryo-EM reconstructions of all components of the XM1 virion and describe the atomic structures of 14 XM1 proteins. The XM1 baseplate is composed of a central hub surrounded by six wedge modules to which twelve spikes are attached. The XM1 tail contains a fewer number of smaller proteins compared to other reported phage baseplates, depicting the minimum requirements for building an effective cell-envelope-penetrating machine. We describe the tail sheath structure in the pre-infection and post-infection states and its conformational changes during infection. In addition, we report, for the first time, the in situ structure of the phage neck region to near-atomic resolution. Based on these structures, we propose mechanisms of virus assembly and infection.
Collapse
Affiliation(s)
- Zhiqing Wang
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
- National Cryo-EM Facility, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, MD 21701, USA
| | - Andrei Fokine
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Xinwu Guo
- Sansure Biotech Inc., Changsha 410205, China
| | - Wen Jiang
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Michael G. Rossmann
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Richard J. Kuhn
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Zhu-Hua Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- School of Marine Sciences, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Thomas Klose
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| |
Collapse
|
3
|
A. Dowd K, Sirohi D, D. Speer S, VanBlargan LA, Chen RE, Mukherjee S, Whitener BM, Govero J, Aleshnick M, Larman B, Sukupolvi-Petty S, Sevvana M, Miller AS, Klose T, Zheng A, Koenig S, Kielian M, Kuhn RJ, Diamond MS, Pierson TC. prM-reactive antibodies reveal a role for partially mature virions in dengue virus pathogenesis. Proc Natl Acad Sci U S A 2023; 120:e2218899120. [PMID: 36638211 PMCID: PMC9933121 DOI: 10.1073/pnas.2218899120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 11/28/2022] [Indexed: 01/15/2023] Open
Abstract
Cleavage of the flavivirus premembrane (prM) structural protein during maturation can be inefficient. The contribution of partially mature flavivirus virions that retain uncleaved prM to pathogenesis during primary infection is unknown. To investigate this question, we characterized the functional properties of newly-generated dengue virus (DENV) prM-reactive monoclonal antibodies (mAbs) in vitro and using a mouse model of DENV disease. Anti-prM mAbs neutralized DENV infection in a virion maturation state-dependent manner. Alanine scanning mutagenesis and cryoelectron microscopy of anti-prM mAbs in complex with immature DENV defined two modes of attachment to a single antigenic site. In vivo, passive transfer of intact anti-prM mAbs resulted in an antibody-dependent enhancement of disease. However, protection against DENV-induced lethality was observed when the transferred mAbs were genetically modified to inhibit their ability to interact with Fcγ receptors. These data establish that in addition to mature forms of the virus, partially mature infectious prM+ virions can also contribute to pathogenesis during primary DENV infections.
Collapse
Affiliation(s)
- Kimberly A. Dowd
- Viral Pathogenesis Section, Laboratory of Viral Diseases, National Institutes of Health, Bethesda, MD20892
| | - Devika Sirohi
- Department of Biological Sciences, Purdue University, West Lafayette, IN47907
- Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, IN47907
| | - Scott D. Speer
- Viral Pathogenesis Section, Laboratory of Viral Diseases, National Institutes of Health, Bethesda, MD20892
| | - Laura A. VanBlargan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO63110
| | - Rita E. Chen
- Department of Medicine, Washington University School of Medicine, St. Louis, MO63110
| | - Swati Mukherjee
- Viral Pathogenesis Section, Laboratory of Viral Diseases, National Institutes of Health, Bethesda, MD20892
| | - Bradley M. Whitener
- Department of Medicine, Washington University School of Medicine, St. Louis, MO63110
| | - Jennifer Govero
- Department of Medicine, Washington University School of Medicine, St. Louis, MO63110
| | - Maya Aleshnick
- Viral Pathogenesis Section, Laboratory of Viral Diseases, National Institutes of Health, Bethesda, MD20892
| | - Bridget Larman
- Viral Pathogenesis Section, Laboratory of Viral Diseases, National Institutes of Health, Bethesda, MD20892
| | - Soila Sukupolvi-Petty
- Department of Medicine, Washington University School of Medicine, St. Louis, MO63110
| | - Madhumati Sevvana
- Department of Biological Sciences, Purdue University, West Lafayette, IN47907
- Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, IN47907
| | - Andrew S. Miller
- Department of Biological Sciences, Purdue University, West Lafayette, IN47907
- Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, IN47907
| | - Thomas Klose
- Department of Biological Sciences, Purdue University, West Lafayette, IN47907
- Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, IN47907
| | - Aihua Zheng
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY10461
| | | | - Margaret Kielian
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY10461
| | - Richard J. Kuhn
- Department of Biological Sciences, Purdue University, West Lafayette, IN47907
- Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, IN47907
| | - Michael S. Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO63110
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO63110
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO63110
| | - Theodore C. Pierson
- Viral Pathogenesis Section, Laboratory of Viral Diseases, National Institutes of Health, Bethesda, MD20892
| |
Collapse
|
4
|
Sevvana M, Rogers TF, Miller AS, Long F, Klose T, Beutler N, Lai YC, Parren M, Walker LM, Buda G, Burton DR, Rossmann MG, Kuhn RJ. Structural Basis of Zika Virus Specific Neutralization in Subsequent Flavivirus Infections. Viruses 2020; 12:v12121346. [PMID: 33255202 PMCID: PMC7760643 DOI: 10.3390/v12121346] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/19/2020] [Accepted: 11/20/2020] [Indexed: 02/06/2023] Open
Abstract
Zika virus (ZIKV), a mosquito-borne human flavivirus that causes microcephaly and other neurological disorders, has been a recent focus for the development of flavivirus vaccines and therapeutics. We report here a 4.0 Å resolution structure of the mature ZIKV in complex with ADI-30056, a ZIKV-specific human monoclonal antibody (hMAb) isolated from a ZIKV infected donor with a prior dengue virus infection. The structure shows that the hMAb interactions span across the E protein dimers on the virus surface, inhibiting conformational changes required for the formation of infectious fusogenic trimers similar to the hMAb, ZIKV-117. Structure-based functional analysis, and structure and sequence comparisons, identified ZIKV residues essential for neutralization and crucial for the evolution of highly potent E protein crosslinking Abs in ZIKV. Thus, this epitope, ZIKV’s “Achilles heel”, defined by the contacts between ZIKV and ADI-30056, could be a suitable target for the design of therapeutic antibodies.
Collapse
Affiliation(s)
- Madhumati Sevvana
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (M.S.); (A.S.M.); (F.L.); (T.K.); (G.B.); (M.G.R.)
| | - Thomas F. Rogers
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; (T.F.R.); (N.B.); (Y.-C.L.); (M.P.); (D.R.B.)
| | - Andrew S. Miller
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (M.S.); (A.S.M.); (F.L.); (T.K.); (G.B.); (M.G.R.)
| | - Feng Long
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (M.S.); (A.S.M.); (F.L.); (T.K.); (G.B.); (M.G.R.)
| | - Thomas Klose
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (M.S.); (A.S.M.); (F.L.); (T.K.); (G.B.); (M.G.R.)
| | - Nathan Beutler
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; (T.F.R.); (N.B.); (Y.-C.L.); (M.P.); (D.R.B.)
| | - Yen-Chung Lai
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; (T.F.R.); (N.B.); (Y.-C.L.); (M.P.); (D.R.B.)
| | - Mara Parren
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; (T.F.R.); (N.B.); (Y.-C.L.); (M.P.); (D.R.B.)
| | | | - Geeta Buda
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (M.S.); (A.S.M.); (F.L.); (T.K.); (G.B.); (M.G.R.)
| | - Dennis R. Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; (T.F.R.); (N.B.); (Y.-C.L.); (M.P.); (D.R.B.)
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
| | - Michael G. Rossmann
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (M.S.); (A.S.M.); (F.L.); (T.K.); (G.B.); (M.G.R.)
| | - Richard J. Kuhn
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; (M.S.); (A.S.M.); (F.L.); (T.K.); (G.B.); (M.G.R.)
- Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA
- Correspondence:
| |
Collapse
|
5
|
Sun C, Gonzalez B, Vago FS, Jiang W. High resolution single particle Cryo-EM refinement using JSPR. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 160:37-42. [PMID: 32622834 DOI: 10.1016/j.pbiomolbio.2020.05.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 05/06/2020] [Accepted: 05/09/2020] [Indexed: 11/30/2022]
Abstract
JSPR is a single particle cryo-EM image processing and 3D reconstruction software developed in the Jiang laboratory at Purdue University. It began as a few refinement scripts for symmetric and asymmetric reconstructions of icosahedral viruses, but has grown into a comprehensive suite of tools for building ab initio reconstructions, high resolution refinements of viruses, protein complexes of arbitrary symmetries including helical tubes/filaments, and image file handling utilities. In this review, we will present examples achieved using JSPR and demonstrate recently implemented features of JSPR such as multi-aberration "alignments" and automatic optimization of masking for the assessment of map resolution using "true" FSC.
Collapse
Affiliation(s)
- Chen Sun
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, 47906, USA
| | - Brenda Gonzalez
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, 47906, USA
| | - Frank S Vago
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, 47906, USA
| | - Wen Jiang
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN, 47906, USA.
| |
Collapse
|
6
|
Kaelber JT, Jiang W, Weaver SC, Auguste AJ, Chiu W. Arrangement of the Polymerase Complexes inside a Nine-Segmented dsRNA Virus. Structure 2020; 28:604-612.e3. [PMID: 32049031 PMCID: PMC7289189 DOI: 10.1016/j.str.2020.01.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 12/18/2019] [Accepted: 01/17/2020] [Indexed: 12/15/2022]
Abstract
Members of the family Reoviridae package several copies of the viral polymerase complex into their capsid to carry out replication and transcription within viral particles. Classical single-particle reconstruction encounters difficulties resolving structures such as the intraparticle polymerase complex because refinement can converge to an incorrect map and because the map could depict a nonrepresentative subset of particles or an average of heterogeneous particles. Using the nine-segmented Fako virus, we tested hypotheses for the arrangement and number of polymerase complexes within the virion by measuring how well each hypothesis describes the set of cryoelectron microscopy images of individual viral particles. We find that the polymerase complex in Fako virus binds at ten possible sites despite having only nine genome segments. A single asymmetric configuration describes the arrangement of these complexes in both virions and genome-free capsids. Similarities between the arrangements of Reoviridae with 9, 10, and 11 segments indicate the generalizability of this architecture.
Collapse
Affiliation(s)
- Jason T Kaelber
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
| | - Wen Jiang
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Scott C Weaver
- Institute for Human Infections and Immunity, World Reference Center for Emerging Viruses and Arboviruses, Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Albert J Auguste
- Institute for Human Infections and Immunity, World Reference Center for Emerging Viruses and Arboviruses, Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Department of Entomology, Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Wah Chiu
- Department of Bioengineering, Department of Microbiology and Immunology, and James H. Clark Center, Stanford University, Stanford, CA, USA
| |
Collapse
|
7
|
Zivanov J, Nakane T, Scheres SHW. Estimation of high-order aberrations and anisotropic magnification from cryo-EM data sets in RELION-3.1. IUCRJ 2020; 7:253-267. [PMID: 32148853 PMCID: PMC7055373 DOI: 10.1107/s2052252520000081] [Citation(s) in RCA: 446] [Impact Index Per Article: 111.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/06/2020] [Indexed: 05/21/2023]
Abstract
Methods are presented that detect three types of aberrations in single-particle cryo-EM data sets: symmetrical and antisymmetrical optical aberrations and magnification anisotropy. Because these methods only depend on the availability of a preliminary 3D reconstruction from the data, they can be used to correct for these aberrations for any given cryo-EM data set, a posteriori. Using five publicly available data sets, it is shown that considering these aberrations improves the resolution of the 3D reconstruction when these effects are present. The methods are implemented in version 3.1 of the open-source software package RELION.
Collapse
Affiliation(s)
- Jasenko Zivanov
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, England
- Biozentrum, University of Basel, Switzerland
| | - Takanori Nakane
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, England
| | - Sjors H. W. Scheres
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, England
| |
Collapse
|
8
|
Baggen J, Liu Y, Lyoo H, van Vliet ALW, Wahedi M, de Bruin JW, Roberts RW, Overduin P, Meijer A, Rossmann MG, Thibaut HJ, van Kuppeveld FJM. Bypassing pan-enterovirus host factor PLA2G16. Nat Commun 2019; 10:3171. [PMID: 31320648 PMCID: PMC6639302 DOI: 10.1038/s41467-019-11256-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 06/25/2019] [Indexed: 02/06/2023] Open
Abstract
Enteroviruses are a major cause of human disease. Adipose-specific phospholipase A2 (PLA2G16) was recently identified as a pan-enterovirus host factor and potential drug target. In this study, we identify a possible mechanism of PLA2G16 evasion by employing a dual glycan receptor-binding enterovirus D68 (EV-D68) strain. We previously showed that this strain does not strictly require the canonical EV-D68 receptor sialic acid. Here, we employ a haploid screen to identify sulfated glycosaminoglycans (sGAGs) as its second glycan receptor. Remarkably, engagement of sGAGs enables this virus to bypass PLA2G16. Using cryo-EM analysis, we reveal that, in contrast to sialic acid, sGAGs stimulate genome release from virions via structural changes that enlarge the putative openings for genome egress. Together, we describe an enterovirus that can bypass PLA2G16 and identify additional virion destabilization as a potential mechanism to circumvent PLA2G16.
Collapse
Affiliation(s)
- Jim Baggen
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL, Utrecht, The Netherlands
| | - Yue Liu
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Heyrhyoung Lyoo
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL, Utrecht, The Netherlands
| | - Arno L W van Vliet
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL, Utrecht, The Netherlands
| | - Maryam Wahedi
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL, Utrecht, The Netherlands
| | - Jost W de Bruin
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL, Utrecht, The Netherlands
| | - Richard W Roberts
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL, Utrecht, The Netherlands
| | - Pieter Overduin
- Virology Division, Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute for Public Health and the Environment, 3720 BA, Bilthoven, The Netherlands
| | - Adam Meijer
- Virology Division, Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute for Public Health and the Environment, 3720 BA, Bilthoven, The Netherlands
| | - Michael G Rossmann
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Hendrik Jan Thibaut
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL, Utrecht, The Netherlands
| | - Frank J M van Kuppeveld
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL, Utrecht, The Netherlands.
| |
Collapse
|
9
|
Li K, Sun C, Klose T, Irimia-Dominguez J, Vago FS, Vidal R, Jiang W. Sub-3 Å apoferritin structure determined with full range of phase shifts using a single position of volta phase plate. J Struct Biol 2019; 206:225-232. [PMID: 30928614 DOI: 10.1016/j.jsb.2019.03.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 03/19/2019] [Accepted: 03/22/2019] [Indexed: 01/06/2023]
Abstract
Volta Phase Plate (VPP) has become an invaluable tool for cryo-EM structural determination of small protein complexes by increasing image contrast. Currently, the standard protocol of VPP usage periodically changes the VPP position to a fresh spot during data collection. Such a protocol was to target the phase shifts to a relatively narrow range (around 90°) based on the observations of increased phase shifts and image blur associated with more images taken with a single VPP position. Here, we report a 2.87 Å resolution structure of apoferritin reconstructed from a dataset collected using only a single position of VPP. The reconstruction resolution and map density features are nearly identical to the reconstruction from the control dataset collected with periodic change of VPP positions. Further experiments have verified that similar results, including a 2.5 Å resolution structure, could be obtained with a full range of phase shifts, different spots of variable phase shift increasing rates, and at different ages of the VPP post-installation. Furthermore, we have found that the phase shifts at low resolutions, probably related to the finite size of the Volta spots, could not be correctly modeled by current CTF model using a constant phase shift at all frequencies. In dataset III, severe beam tilt issue was identified but could be computationally corrected with iterative refinements. The observations in this study may provide new insights into further improvement of both the efficiency and robustness of VPP, and to help turn VPP into a plug-and-play device for high-resolution cryo-EM.
Collapse
Affiliation(s)
- Kunpeng Li
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN 47906, USA
| | - Chen Sun
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN 47906, USA
| | - Thomas Klose
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN 47906, USA
| | - Jose Irimia-Dominguez
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Frank S Vago
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN 47906, USA
| | - Ruben Vidal
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Wen Jiang
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN 47906, USA.
| |
Collapse
|
10
|
Ananthaswamy N, Fang Q, AlSalmi W, Jain S, Chen Z, Klose T, Sun Y, Liu Y, Mahalingam M, Chand S, Tovanabutra S, Robb ML, Rossmann MG, Rao VB. A sequestered fusion peptide in the structure of an HIV-1 transmitted founder envelope trimer. Nat Commun 2019; 10:873. [PMID: 30787293 PMCID: PMC6382815 DOI: 10.1038/s41467-019-08825-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 02/01/2019] [Indexed: 12/23/2022] Open
Abstract
The envelope protein of human immunodeficiency virus-1 (HIV-1) and its fusion peptide are essential for cell entry and vaccine design. Here, we describe the 3.9-Å resolution structure of an envelope protein trimer from a very early transmitted founder virus (CRF01_AE T/F100) complexed with Fab from the broadly neutralizing antibody (bNAb) 8ANC195. The overall T/F100 trimer structure is similar to other reported "closed" state prefusion trimer structures. In contrast, the fusion peptide, which is exposed to solvent in reported closed structures, is sequestered (buried) in the hydrophobic core of the T/F100 trimer. A buried conformation has previously been observed in "open" state structures formed after CD4 receptor binding. The T/F100 trimer binds poorly to bNAbs including the fusion peptide-specific bNAbs PGT151 and VRC34.01. The T/F100 structure might represent a prefusion state, intermediate between the closed and open states. These observations are relevant to mechanisms of HIV-1 transmission and vaccine design.
Collapse
Affiliation(s)
- Neeti Ananthaswamy
- Department of Biology, The Catholic University of America, Washington, DC, 20064, USA
| | - Qianglin Fang
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Wadad AlSalmi
- Department of Biology, The Catholic University of America, Washington, DC, 20064, USA
| | - Swati Jain
- Department of Biology, The Catholic University of America, Washington, DC, 20064, USA
| | - Zhenguo Chen
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.,The Fifth People's Hospital of Shanghai & Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, People's Republic of China
| | - Thomas Klose
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Yingyuan Sun
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Yue Liu
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Marthandan Mahalingam
- Department of Biology, The Catholic University of America, Washington, DC, 20064, USA
| | - Subhash Chand
- Department of Biology, The Catholic University of America, Washington, DC, 20064, USA
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, MD, 20910, USA
| | - Merlin L Robb
- U.S. Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, Silver Spring, MD, 20910, USA
| | - Michael G Rossmann
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.
| | - Venigalla B Rao
- Department of Biology, The Catholic University of America, Washington, DC, 20064, USA.
| |
Collapse
|
11
|
Coxsackievirus A10 atomic structure facilitating the discovery of a broad-spectrum inhibitor against human enteroviruses. Cell Discov 2019; 5:4. [PMID: 30652025 PMCID: PMC6331555 DOI: 10.1038/s41421-018-0073-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 10/22/2018] [Accepted: 10/22/2018] [Indexed: 01/21/2023] Open
Abstract
Coxsackievirus A10 (CV-A10) belongs to the Enterovirus species A and is a causative agent of hand, foot, and mouth disease. Here we present cryo-EM structures of CV-A10 mature virion and native empty particle (NEP) at 2.84 and 3.12 Å, respectively. Our CV-A10 mature virion structure reveals a density corresponding to a lipidic pocket factor of 18 carbon atoms in the hydrophobic pocket formed within viral protein 1. By structure-guided high-throughput drug screening and subsequent verification in cell-based infection-inhibition assays, we identified four compounds that inhibited CV-A10 infection in vitro. These compounds represent a new class of anti-enteroviral drug leads. Notably, one of the compounds, ICA135, also exerted broad-spectrum inhibitory effects on a number of representative viruses from all four species (A–D) of human enteroviruses. Our findings should facilitate the development of broadly effective drugs and vaccines for enterovirus infections.
Collapse
|
12
|
Structural basis of a potent human monoclonal antibody against Zika virus targeting a quaternary epitope. Proc Natl Acad Sci U S A 2019; 116:1591-1596. [PMID: 30642974 DOI: 10.1073/pnas.1815432116] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Zika virus (ZIKV) is a major human pathogen and member of the Flavivirus genus in the Flaviviridae family. In contrast to most other insect-transmitted flaviviruses, ZIKV also can be transmitted sexually and from mother to fetus in humans. During recent outbreaks, ZIKV infections have been linked to microcephaly, congenital disease, and Guillain-Barré syndrome. Neutralizing antibodies have potential as therapeutic agents. We report here a 4-Å-resolution cryo-electron microscopy structure of the ZIKV virion in complex with Fab fragments of the potently neutralizing human monoclonal antibody ZIKV-195. The footprint of the ZIKV-195 Fab fragment expands across two adjacent envelope (E) protein protomers. ZIKV neutralization by this antibody is presumably accomplished by cross-linking the E proteins, which likely prevents formation of E protein trimers required for fusion of the viral and cellular membranes. A single dose of ZIKV-195 administered 5 days after virus inoculation showed marked protection against lethality in a stringent mouse model of infection.
Collapse
|
13
|
Molecular basis for the acid-initiated uncoating of human enterovirus D68. Proc Natl Acad Sci U S A 2018; 115:E12209-E12217. [PMID: 30530701 DOI: 10.1073/pnas.1803347115] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Enterovirus D68 (EV-D68) belongs to a group of enteroviruses that contain a single positive-sense RNA genome surrounded by an icosahedral capsid. Like common cold viruses, EV-D68 mainly causes respiratory infections and is acid-labile. The molecular mechanism by which the acid-sensitive EV-D68 virions uncoat and deliver their genome into a host cell is unknown. Using cryoelectron microscopy (cryo-EM), we have determined the structures of the full native virion and an uncoating intermediate [the A (altered) particle] of EV-D68 at 2.2- and 2.7-Å resolution, respectively. These structures showed that acid treatment of EV-D68 leads to particle expansion, externalization of the viral protein VP1 N termini from the capsid interior, and formation of pores around the icosahedral twofold axes through which the viral RNA can exit. Moreover, because of the low stability of EV-D68, cryo-EM analyses of a mixed population of particles at neutral pH and following acid treatment demonstrated the involvement of multiple structural intermediates during virus uncoating. Among these, a previously undescribed state, the expanded 1 ("E1") particle, shows a majority of internal regions (e.g., the VP1 N termini) to be ordered as in the full native virion. Thus, the E1 particle acts as an intermediate in the transition from full native virions to A particles. Together, the present work delineates the pathway of EV-D68 uncoating and provides the molecular basis for the acid lability of EV-D68 and of the related common cold viruses.
Collapse
|
14
|
Sevvana M, Long F, Miller AS, Klose T, Buda G, Sun L, Kuhn RJ, Rossmann MG. Refinement and Analysis of the Mature Zika Virus Cryo-EM Structure at 3.1 Å Resolution. Structure 2018; 26:1169-1177.e3. [PMID: 29958768 PMCID: PMC6125166 DOI: 10.1016/j.str.2018.05.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 04/26/2018] [Accepted: 05/14/2018] [Indexed: 02/07/2023]
Abstract
Among the several arthropod-borne human flaviviral diseases, the recent outbreak of Zika virus (ZIKV) has caused devastating birth defects and neurological disorders, challenging the world with another major public health concern. We report here the refined structure of the mature ZIKV at a resolution of 3.1 Å as determined by cryo-electron microscopic single-particle reconstruction. The improvement in the resolution, compared with previous enveloped virus structures, was the result of optimized virus preparation methods and data processing techniques. The glycoprotein interactions and surface properties of ZIKV were compared with other mosquito-borne flavivirus structures. The largest structural differences and sequence variations occur at the glycosylation loop associated with receptor binding. Probable drug binding pockets were identified on the viral surface. These results also provide a structural basis for the design of vaccines against ZIKV.
Collapse
Affiliation(s)
- Madhumati Sevvana
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Feng Long
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Andrew S Miller
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Thomas Klose
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Geeta Buda
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Lei Sun
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Richard J Kuhn
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Michael G Rossmann
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.
| |
Collapse
|
15
|
Mei K, Li Y, Wang S, Shao G, Wang J, Ding Y, Luo G, Yue P, Liu JJ, Wang X, Dong MQ, Wang HW, Guo W. Cryo-EM structure of the exocyst complex. Nat Struct Mol Biol 2018; 25:139-146. [PMID: 29335562 PMCID: PMC5971111 DOI: 10.1038/s41594-017-0016-2] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 12/07/2017] [Indexed: 12/22/2022]
Abstract
The exocyst is an evolutionarily conserved octameric protein complex that mediates the tethering of post-Golgi secretory vesicles to the plasma membrane during exocytosis and is implicated in many cellular processes such as cell polarization, cytokinesis, ciliogenesis and tumor invasion. Using cryo-EM and chemical cross-linking MS (CXMS), we solved the structure of the Saccharomyces cerevisiae exocyst complex at an average resolution of 4.4 Å. Our model revealed the architecture of the exocyst and led to the identification of the helical bundles that mediate the assembly of the complex at its core. Sequence analysis suggests that these regions are evolutionarily conserved across eukaryotic systems. Additional cell biological data suggest a mechanism for exocyst assembly that leads to vesicle tethering at the plasma membrane.
Collapse
Affiliation(s)
- Kunrong Mei
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Yan Li
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua University, Beijing, China.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
| | - Shaoxiao Wang
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Guangcan Shao
- National Institute of Biological Sciences, Beijing, China
| | - Jia Wang
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua University, Beijing, China.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
| | - Yuehe Ding
- National Institute of Biological Sciences, Beijing, China
| | - Guangzuo Luo
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Peng Yue
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Jun-Jie Liu
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua University, Beijing, China.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Xinquan Wang
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua University, Beijing, China.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, China
| | - Hong-Wei Wang
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua University, Beijing, China. .,Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China. .,School of Life Sciences, Tsinghua University, Beijing, China. .,Tsinghua-Peking Joint Center for Life Sciences, Beijing, China.
| | - Wei Guo
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
16
|
Yan R, Li K, Jiang W. Defocus and magnification dependent variation of TEM image astigmatism. Sci Rep 2018; 8:344. [PMID: 29321616 PMCID: PMC5762780 DOI: 10.1038/s41598-017-18820-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 12/18/2017] [Indexed: 11/09/2022] Open
Abstract
Daily alignment of the microscope is a prerequisite to reaching optimal lens conditions for high resolution imaging in cryo-EM. In this study, we have investigated how image astigmatism varies with the imaging conditions (e.g. defocus, magnification). We have found that the large change of defocus/magnification between visual correction of astigmatism and subsequent data collection tasks, or during data collection, will inevitably result in undesirable astigmatism in the final images. The dependence of astigmatism on the imaging conditions varies significantly from time to time, so that it cannot be reliably compensated by pre-calibration of the microscope. Based on these findings, we recommend that the same magnification and the median defocus of the intended defocus range for final data collection are used in the objective lens astigmatism correction task during microscope alignment and in the focus mode of the iterative low-dose imaging. It is also desirable to develop a fast, accurate method that can perform dynamic correction of the astigmatism for different intended defocuses during automated imaging. Our findings also suggest that the slope of astigmatism changes caused by varying defocuses can be used as a convenient measurement of objective lens rotation symmetry and potentially an acceptance test of new electron microscopes.
Collapse
Affiliation(s)
- Rui Yan
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Kunpeng Li
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Wen Jiang
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA.
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, 47907, USA.
| |
Collapse
|
17
|
A 3.0-Angstrom Resolution Cryo-Electron Microscopy Structure and Antigenic Sites of Coxsackievirus A6-Like Particles. J Virol 2018; 92:JVI.01257-17. [PMID: 29093091 DOI: 10.1128/jvi.01257-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 09/28/2017] [Indexed: 02/06/2023] Open
Abstract
Coxsackievirus A6 (CVA6) has recently emerged as one of the predominant causative agents of hand, foot, and mouth disease (HFMD). The structure of the CVA6 mature viral particle has not been solved thus far. Our previous work shows that recombinant virus-like particles (VLPs) of CVA6 represent a promising CVA6 vaccine candidate. Here, we report the first cryo-electron microscopy (cryo-EM) structure of the CVA6 VLP at 3.0-Å resolution. The CVA6 VLP exhibits the characteristic features of enteroviruses but presents an open channel at the 2-fold axis and an empty, collapsed VP1 pocket, which is broadly similar to the structures of the enterovirus 71 (EV71) VLP and coxsackievirus A16 (CVA16) 135S expanded particle, indicating that the CVA6 VLP is in an expanded conformation. Structural comparisons reveal that two common salt bridges within protomers are maintained in the CVA6 VLP and other viruses of the Enterovirus genus, implying that these salt bridges may play a critical role in enteroviral protomer assembly. However, there are apparent structural differences among the CVA6 VLP, EV71 VLP, and CVA16 135S particle in the surface-exposed loops and C termini of subunit proteins, which are often antigenic sites for enteroviruses. By immunological assays, we identified two CVA6-specific linear B-cell epitopes (designated P42 and P59) located at the GH loop and the C-terminal region of VP1, respectively, in agreement with the structure-based prediction of antigenic sites. Our findings elucidate the structural basis and important antigenic sites of the CVA6 VLP as a strong vaccine candidate and also provide insight into enteroviral protomer assembly.IMPORTANCE Coxsackievirus A6 (CVA6) is becoming one of the major pathogens causing hand, foot, and mouth disease (HFMD), leading to significant morbidity and mortality in children and adults. However, no vaccine is currently available to prevent CVA6 infection. Our previous work shows that recombinant virus-like particles (VLPs) of CVA6 are a promising CVA6 vaccine candidate. Here, we present a 3.0-Å structure of the CVA6 VLP determined by cryo-electron microscopy. The overall architecture of the CVA6 VLP is similar to those of the expanded structures of enterovirus 71 (EV71) and coxsackievirus A16 (CVA16), but careful structural comparisons reveal significant differences in the surface-exposed loops and C termini of each capsid protein of these particles. In addition, we identified two CVA6-specific linear B-cell epitopes and mapped them to the GH loop and the C-terminal region of VP1, respectively. Collectively, our findings provide a structural basis and important antigenic information for CVA6 VLP vaccine development.
Collapse
|
18
|
Wang Z, Hardies SC, Fokine A, Klose T, Jiang W, Cho BC, Rossmann MG. Structure of the Marine Siphovirus TW1: Evolution of Capsid-Stabilizing Proteins and Tail Spikes. Structure 2017; 26:238-248.e3. [PMID: 29290487 DOI: 10.1016/j.str.2017.12.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 10/16/2017] [Accepted: 12/01/2017] [Indexed: 01/08/2023]
Abstract
Marine bacteriophage TW1 belongs to the Siphoviridae family and infects Pseudoalteromonas phenolica. Mass spectrometry analysis has identified 16 different proteins in the TW1 virion. Functions of most of these proteins have been predicted by bioinformatic methods. A 3.6 Å resolution cryoelectron microscopy map of the icosahedrally averaged TW1 head showed the atomic structures of the major capsid protein, gp57∗, and the capsid-stabilizing protein, gp56. The gp57∗ structure is similar to that of the phage HK97 capsid protein. The gp56 protein has two domains, each having folds similar to that of the N-terminal part of phage λ gpD, indicating a common ancestry. The first gp56 domain clamps adjacent capsomers together, whereas the second domain is required for trimerization. A 6-fold-averaged reconstruction of the distal part of the tail showed that TW1 has six tail spikes, which are unusual for siphophages but are similar to the podophages P22 and Sf6, suggesting a common evolutionary origin of these spikes.
Collapse
Affiliation(s)
- Zhiqing Wang
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Stephen C Hardies
- Department of Biochemistry, The University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Andrei Fokine
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Thomas Klose
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Wen Jiang
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Byung Cheol Cho
- School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul 151-742, Korea
| | - Michael G Rossmann
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.
| |
Collapse
|
19
|
Sherman MB, Kakani K, Rochon D, Jiang W, Voss NR, Smith TJ. Stability of Cucumber Necrosis Virus at the Quasi-6-Fold Axis Affects Zoospore Transmission. J Virol 2017; 91:e01030-17. [PMID: 28724762 PMCID: PMC5599764 DOI: 10.1128/jvi.01030-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 07/12/2017] [Indexed: 11/20/2022] Open
Abstract
Cucumber necrosis virus (CNV) is a member of the genus Tombusvirus and has a monopartite positive-sense RNA genome. CNV is transmitted in nature via zoospores of the fungus Olpidium bornovanus As with other members of the Tombusvirus genus, the CNV capsid swells when exposed to alkaline pH and EDTA. We previously demonstrated that a P73G mutation blocks the virus from zoospore transmission while not significantly affecting replication in plants (K. Kakani, R. Reade, and D. Rochon, J Mol Biol 338:507-517, 2004, https://doi.org/10.1016/j.jmb.2004.03.008). P73 lies immediately adjacent to a putative zinc binding site (M. Li et al., J Virol 87:12166-12175, 2013, https://doi.org/10.1128/JVI.01965-13) that is formed by three icosahedrally related His residues in the N termini of the C subunit at the quasi-6-fold axes. To better understand how this buried residue might affect vector transmission, we determined the cryo-electron microscopy structure of wild-type CNV in the native and swollen state and of the transmission-defective mutant, P73G, under native conditions. With the wild-type CNV, the swollen structure demonstrated the expected expansion of the capsid. However, the zinc binding region at the quasi-6-fold at the β-annulus axes remained intact. By comparison, the zinc binding region of the P73G mutant, even under native conditions, was markedly disordered, suggesting that the β-annulus had been disrupted and that this could destabilize the capsid. This was confirmed with pH and urea denaturation experiments in conjunction with electron microscopy analysis. We suggest that the P73G mutation affects the zinc binding and/or the β-annulus, making it more fragile under neutral/basic pH conditions. This, in turn, may affect zoospore transmission.IMPORTANCECucumber necrosis virus (CNV), a member of the genus Tombusvirus, is transmitted in nature via zoospores of the fungus Olpidium bornovanus While a number of plant viruses are transmitted via insect vectors, little is known at the molecular level as to how the viruses are recognized and transmitted. As with many spherical plant viruses, the CNV capsid swells when exposed to alkaline pH and EDTA. We previously demonstrated that a P73G mutation that lies inside the capsid immediately adjacent to a putative zinc binding site (Li et al., J Virol 87:12166-12175, 2013, https://doi.org/10.1128/JVI.01965-13) blocks the virus from zoospore transmission while not significantly affecting replication in plants (K. Kakani, R. Reade, and D. Rochon, J Mol Biol 338:507-517, 2004, https://doi.org/10.1016/j.jmb.2004.03.008). Here, we show that the P73G mutant is less stable than the wild type, and this appears to be correlated with destabilization of the β-annulus at the icosahedral 3-fold axes. Therefore, the β-annulus appears not to be essential for particle assembly but is necessary for interactions with the transmission vector.
Collapse
Affiliation(s)
- Michael B Sherman
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| | - Kishore Kakani
- Pacific Agri-Food Research Centre, Agriculture and Agri-Food Canada, Summerland, British Columbia, Canada
| | - D'Ann Rochon
- Pacific Agri-Food Research Centre, Agriculture and Agri-Food Canada, Summerland, British Columbia, Canada
| | - Wen Jiang
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Neil R Voss
- Department of Biology, Roosevelt University, Chicago, Illinois, USA
| | - Thomas J Smith
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| |
Collapse
|
20
|
Jiang W, Tang L. Atomic cryo-EM structures of viruses. Curr Opin Struct Biol 2017; 46:122-129. [PMID: 28787658 PMCID: PMC5683926 DOI: 10.1016/j.sbi.2017.07.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/12/2017] [Accepted: 07/19/2017] [Indexed: 01/30/2023]
Abstract
During the development of single particle cryo-EM in past five decades, icosahedral viruses have led the resolution progress owing to their large mass and high symmetry. Many technical advances in cryo-EM were first established with viruses. Since reaching ∼4Å resolution in 2008, it has become a relatively routine task to solve the atomic structure of isolated viruses. The future of structural virology will be increasingly focused on remaining challenges including solving structures of jumbo viruses, intermediate functional states during assembly, maturation, and infection, and in situ structures. Recent demonstrations of near-atomic resolution structure with electron tomography and sub-tomogram averaging opens a new direction for high resolution studies of pleomorphic viruses and the pleomorphic states of icosahedral viruses that have defied past efforts using the single particle cryo-EM approach.
Collapse
Affiliation(s)
- Wen Jiang
- Department of Biological Sciences, Immunology and Infectious Disease, Purdue University, 240 S. Martin Jischke Drive, West Lafayette, IN 47907, USA; Department of Chemistry, Immunology and Infectious Disease, Purdue University, 240 S. Martin Jischke Drive, West Lafayette, IN 47907, USA; Markey Center for Structural Biology, Immunology and Infectious Disease, Purdue University, 240 S. Martin Jischke Drive, West Lafayette, IN 47907, USA; Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, 240 S. Martin Jischke Drive, West Lafayette, IN 47907, USA.
| | - Liang Tang
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA.
| |
Collapse
|
21
|
Cryo-EM structure of the bacteriophage T4 isometric head at 3.3-Å resolution and its relevance to the assembly of icosahedral viruses. Proc Natl Acad Sci U S A 2017; 114:E8184-E8193. [PMID: 28893988 DOI: 10.1073/pnas.1708483114] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The 3.3-Å cryo-EM structure of the 860-Å-diameter isometric mutant bacteriophage T4 capsid has been determined. WT T4 has a prolate capsid characterized by triangulation numbers (T numbers) Tend = 13 for end caps and Tmid = 20 for midsection. A mutation in the major capsid protein, gp23, produced T=13 icosahedral capsids. The capsid is stabilized by 660 copies of the outer capsid protein, Soc, which clamp adjacent gp23 hexamers. The occupancies of Soc molecules are proportional to the size of the angle between the planes of adjacent hexameric capsomers. The angle between adjacent hexameric capsomers is greatest around the fivefold vertices, where there is the largest deviation from a planar hexagonal array. Thus, the Soc molecules reinforce the structure where there is the greatest strain in the gp23 hexagonal lattice. Mutations that change the angles between adjacent capsomers affect the positions of the pentameric vertices, resulting in different triangulation numbers in bacteriophage T4. The analysis of the T4 mutant head assembly gives guidance to how other icosahedral viruses reproducibly assemble into capsids with a predetermined T number, although the influence of scaffolding proteins is also important.
Collapse
|
22
|
Yu G, Li K, Huang P, Jiang X, Jiang W. Antibody-Based Affinity Cryoelectron Microscopy at 2.6-Å Resolution. Structure 2017; 24:1984-1990. [PMID: 27806259 DOI: 10.1016/j.str.2016.09.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/16/2016] [Accepted: 09/30/2016] [Indexed: 02/02/2023]
Abstract
The affinity cryoelectron microscopy (cryo-EM) approach has been explored in recent years to simplify and/or improve the sample preparation for cryo-EM, which can bring previously challenging specimens such as those of low abundance and/or unpurified ones within reach of the cryo-EM technique. Despite the demonstrated successes for solving structures to low to intermediate resolutions, the lack of near-atomic structures using this approach has led to a common perception of affinity cryo-EM as a niche technique incapable of reaching high resolutions. Here, we report a ∼2.6-Å structure solved using the antibody-based affinity grid approach with low-concentration Tulane virus purified from a low-yield cell-culture system that has been challenging to standard cryo-EM grid preparation. Quantitative analyses of the structure indicate data and reconstruction quality comparable with the conventional grid preparation method using samples at high concentration.
Collapse
Affiliation(s)
- Guimei Yu
- Department of Biological Science, Markey Center for Structural Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Kunpeng Li
- Department of Biological Science, Markey Center for Structural Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Pengwei Huang
- Divisions of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Xi Jiang
- Divisions of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Wen Jiang
- Department of Biological Science, Markey Center for Structural Biology, Purdue University, West Lafayette, IN 47907, USA.
| |
Collapse
|
23
|
Abstract
Rhinoviruses (RVs) are the major causes of common colds in humans. They have a nonenveloped, icosahedral capsid surrounding a positive-strand RNA genome. Here we report that the antigen-binding (Fab) fragment of a neutralizing antibody (C5) can trigger genome release from RV-B14 to form emptied particles and neutralize virus infection. Using cryo-electron microscopy, structures of the C5 Fab in complex with the full and emptied particles have been determined at 2.3 Å and 3.0 Å resolution, respectively. Each of the 60 Fab molecules binds primarily to a region on viral protein 3 (VP3). Binding of the C5 Fabs to RV-B14 results in significant conformational changes around holes in the capsid through which the viral RNA might exit. These results are so far the highest resolution view of an antibody-virus complex and elucidate a mechanism whereby antibodies neutralize RVs and related viruses by inducing virus uncoating.
Collapse
|
24
|
Structure of a headful DNA-packaging bacterial virus at 2.9 Å resolution by electron cryo-microscopy. Proc Natl Acad Sci U S A 2017; 114:3601-3606. [PMID: 28320961 DOI: 10.1073/pnas.1615025114] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The enormous prevalence of tailed DNA bacteriophages on this planet is enabled by highly efficient self-assembly of hundreds of protein subunits into highly stable capsids. These capsids can stand with an internal pressure as high as ∼50 atmospheres as a result of the phage DNA-packaging process. Here we report the complete atomic model of the headful DNA-packaging bacteriophage Sf6 at 2.9 Å resolution determined by electron cryo-microscopy. The structure reveals the DNA-inflated, tensed state of a robust protein shell assembled via noncovalent interactions. Remarkable global conformational polymorphism of capsid proteins, a network formed by extended N arms, mortise-and-tenon-like intercapsomer joints, and abundant β-sheet-like mainchain:mainchain intermolecular interactions, confers significant strength yet also flexibility required for capsid assembly and DNA packaging. Differential formations of the hexon and penton are mediated by a drastic α-helix-to-β-strand structural transition. The assembly scheme revealed here may be common among tailed DNA phages and herpesviruses.
Collapse
|
25
|
A human antibody against Zika virus crosslinks the E protein to prevent infection. Nat Commun 2017; 8:14722. [PMID: 28300075 PMCID: PMC5356071 DOI: 10.1038/ncomms14722] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 01/24/2017] [Indexed: 02/07/2023] Open
Abstract
The recent Zika virus (ZIKV) epidemic has been linked to unusual and severe clinical manifestations including microcephaly in fetuses of infected pregnant women and Guillian-Barré syndrome in adults. Neutralizing antibodies present a possible therapeutic approach to prevent and control ZIKV infection. Here we present a 6.2 Å resolution three-dimensional cryo-electron microscopy (cryoEM) structure of an infectious ZIKV (strain H/PF/2013, French Polynesia) in complex with the Fab fragment of a highly therapeutic and neutralizing human monoclonal antibody, ZIKV-117. The antibody had been shown to prevent fetal infection and demise in mice. The structure shows that ZIKV-117 Fabs cross-link the monomers within the surface E glycoprotein dimers as well as between neighbouring dimers, thus preventing the reorganization of E protein monomers into fusogenic trimers in the acidic environment of endosomes.
Collapse
|
26
|
Han Y, Yan C, Nguyen THD, Jackobel AJ, Ivanov I, Knutson BA, He Y. Structural mechanism of ATP-independent transcription initiation by RNA polymerase I. eLife 2017; 6:e27414. [PMID: 28623663 PMCID: PMC5489313 DOI: 10.7554/elife.27414] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/17/2017] [Indexed: 12/02/2022] Open
Abstract
Transcription initiation by RNA Polymerase I (Pol I) depends on the Core Factor (CF) complex to recognize the upstream promoter and assemble into a Pre-Initiation Complex (PIC). Here, we solve a structure of Saccharomyces cerevisiae Pol I-CF-DNA to 3.8 Å resolution using single-particle cryo-electron microscopy. The structure reveals a bipartite architecture of Core Factor and its recognition of the promoter from -27 to -16. Core Factor's intrinsic mobility correlates well with different conformational states of the Pol I cleft, in addition to the stabilization of either Rrn7 N-terminal domain near Pol I wall or the tandem winged helix domain of A49 at a partially overlapping location. Comparison of the three states in this study with the Pol II system suggests that a ratchet motion of the Core Factor-DNA sub-complex at upstream facilitates promoter melting in an ATP-independent manner, distinct from a DNA translocase actively threading the downstream DNA in the Pol II PIC.
Collapse
Affiliation(s)
- Yan Han
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Chunli Yan
- Department of Chemistry, Georgia State University, Atlanta, United States,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, United States
| | | | - Ashleigh J Jackobel
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, United States
| | - Ivaylo Ivanov
- Department of Chemistry, Georgia State University, Atlanta, United States,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, United States
| | - Bruce A Knutson
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, United States, (BAK)
| | - Yuan He
- Department of Molecular Biosciences, Northwestern University, Evanston, United States, (YHe)
| |
Collapse
|
27
|
Yan R, Li K, Jiang W. Real-time detection and single-pass minimization of TEM objective lens astigmatism. J Struct Biol 2016; 197:210-219. [PMID: 27838367 DOI: 10.1016/j.jsb.2016.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 10/29/2016] [Accepted: 11/04/2016] [Indexed: 11/28/2022]
Abstract
Minimization of the astigmatism of the objective lens is a critical daily instrument alignment task essential for high resolution TEM imaging. Fast and sensitive detection of astigmatism is needed to provide real-time feedback and adjust the stigmators to efficiently reduce astigmatism. Currently the method used by many microscopists is to visually examine the roundness of a diffractogram (Thon rings) and iteratively adjust the stigmators to make the Thon rings circular. This subjective method is limited by poor sensitivity and potentially biased by the astigmatism of human eyes. In this study, an s2 power spectra based method, s2stigmator, was developed to allow fast and sensitive detection of the astigmatism in TEM live images. The "radar"-style display provides real-time feedback to guide the adjustment of the objective lens stigmators. Such unique capability allowed us to discover the mapping of the two stigmators to the astigmatism amplitude and angle, which led us to develop a single-pass tuning strategy capable of significantly quicker minimization of the objective lens astigmatism.
Collapse
Affiliation(s)
- Rui Yan
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Kunpeng Li
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Wen Jiang
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.
| |
Collapse
|