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Membrane-Containing Icosahedral Bacteriophage PRD1: The Dawn of Viral Lineages. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1215:85-109. [DOI: 10.1007/978-3-030-14741-9_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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2
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Quemin ERJ, Quax TEF. Archaeal viruses at the cell envelope: entry and egress. Front Microbiol 2015; 6:552. [PMID: 26097469 PMCID: PMC4456609 DOI: 10.3389/fmicb.2015.00552] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 05/19/2015] [Indexed: 11/13/2022] Open
Abstract
The cell envelope represents the main line of host defense that viruses encounter on their way from one cell to another. The cytoplasmic membrane in general is a physical barrier that needs to be crossed both upon viral entry and exit. Therefore, viruses from the three domains of life employ a wide range of strategies for perforation of the cell membrane, each adapted to the cell surface environment of their host. Here, we review recent insights on entry and egress mechanisms of viruses infecting archaea. Due to the unique nature of the archaeal cell envelope, these particular viruses exhibit novel and unexpected mechanisms to traverse the cellular membrane.
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Affiliation(s)
| | - Tessa E F Quax
- Molecular Biology of Archaea, Institute for Biology II - Microbiology, University of Freiburg , Freiburg, Germany
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3
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Atanasova NS, Senčilo A, Pietilä MK, Roine E, Oksanen HM, Bamford DH. Comparison of lipid-containing bacterial and archaeal viruses. Adv Virus Res 2015; 92:1-61. [PMID: 25701885 DOI: 10.1016/bs.aivir.2014.11.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Lipid-containing bacteriophages were discovered late and considered to be rare. After further phage isolations and the establishment of the domain Archaea, several new prokaryotic viruses with lipids were observed. Consequently, the presence of lipids in prokaryotic viruses is reasonably common. The wealth of information about how prokaryotic viruses use their lipids comes from a few well-studied model viruses (PM2, PRD1, and ϕ6). These bacteriophages derive their lipid membranes selectively from the host during the virion assembly process which, in the case of PM2 and PRD1, culminates in the formation of protein capsid with an inner membrane, and for ϕ6 an outer envelope. Several inner membrane-containing viruses have been described for archaea, and their lipid acquisition models are reminiscent to those of PM2 and PRD1. Unselective acquisition of lipids has been observed for bacterial mycoplasmaviruses and archaeal pleolipoviruses, which resemble each other by size, morphology, and life style. In addition to these shared morphotypes of bacterial and archaeal viruses, archaea are infected by viruses with unique morphotypes, such as lemon-shaped, helical, and globular ones. It appears that structurally related viruses may or may not have a lipid component in the virion, suggesting that the significance of viral lipids might be to provide viruses extended means to interact with the host cell.
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Affiliation(s)
- Nina S Atanasova
- Department of Biosciences and Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Ana Senčilo
- Department of Biosciences and Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Maija K Pietilä
- Department of Biosciences and Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Elina Roine
- Department of Biosciences and Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Hanna M Oksanen
- Department of Biosciences and Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Dennis H Bamford
- Department of Biosciences and Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
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Mattila S, Oksanen HM, Bamford JKH. Probing protein interactions in the membrane-containing virus PRD1. J Gen Virol 2014; 96:453-462. [PMID: 25316797 DOI: 10.1099/vir.0.069187-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PRD1 is a Gram-negative bacteria infecting complex tailless icosahedral virus with an inner membrane. This type virus of the family Tectiviridae contains at least 18 structural protein species, of which several are membrane associated. Vertices of the PRD1 virion consist of complexes recognizing the host cell, except for one special vertex through which the genome is packaged. Despite extensive knowledge of the overall structure of the PRD1 virion and several individual proteins at the atomic level, the locations and interactions of various integral membrane proteins and membrane-associated proteins still remain a mystery. Here, we demonstrated that blue native PAGE can be used to probe protein-protein interactions in complex membrane-containing viruses. Using this technique and PRD1 as a model, we identified the known PRD1 multiprotein vertex structure composed of penton protein P31, spike protein P5, receptor-binding protein P2 and stabilizing protein P16 linking the vertex to the internal membrane. Our results also indicated that two transmembrane proteins, P7 and P14, involved in viral nucleic acid delivery, make a complex. In addition, we performed a zymogram analysis using mutant particles devoid of the special vertex that indicated that the lytic enzyme P15 of PRD1 was not part of the packaging vertex, thus contradicting previously published results.
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Affiliation(s)
- Sari Mattila
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science and Nanoscience Center, PO Box 35, University of Jyväskylä, 40014 Jyväskylä, Finland
| | - Hanna M Oksanen
- Department of Biosciences and Institute of Biotechnology, PO Box 56, University of Helsinki, 00014 Helsinki, Finland
| | - Jaana K H Bamford
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science and Nanoscience Center, PO Box 35, University of Jyväskylä, 40014 Jyväskylä, Finland
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Peralta B, Gil-Carton D, Castaño-Díez D, Bertin A, Boulogne C, Oksanen HM, Bamford DH, Abrescia NGA. Mechanism of membranous tunnelling nanotube formation in viral genome delivery. PLoS Biol 2013; 11:e1001667. [PMID: 24086111 PMCID: PMC3782422 DOI: 10.1371/journal.pbio.1001667] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 08/15/2013] [Indexed: 11/19/2022] Open
Abstract
In internal membrane-containing viruses, a lipid vesicle enclosed by the icosahedral capsid protects the genome. It has been postulated that this internal membrane is the genome delivery device of the virus. Viruses built with this architectural principle infect hosts in all three domains of cellular life. Here, using a combination of electron microscopy techniques, we investigate bacteriophage PRD1, the best understood model for such viruses, to unveil the mechanism behind the genome translocation across the cell envelope. To deliver its double-stranded DNA, the icosahedral protein-rich virus membrane transforms into a tubular structure protruding from one of the 12 vertices of the capsid. We suggest that this viral nanotube exits from the same vertex used for DNA packaging, which is biochemically distinct from the other 11. The tube crosses the capsid through an aperture corresponding to the loss of the peripentonal P3 major capsid protein trimers, penton protein P31 and membrane protein P16. The remodeling of the internal viral membrane is nucleated by changes in osmolarity and loss of capsid-membrane interactions as consequence of the de-capping of the vertices. This engages the polymerization of the tail tube, which is structured by membrane-associated proteins. We have observed that the proteo-lipidic tube in vivo can pierce the gram-negative bacterial cell envelope allowing the viral genome to be shuttled to the host cell. The internal diameter of the tube allows one double-stranded DNA chain to be translocated. We conclude that the assembly principles of the viral tunneling nanotube take advantage of proteo-lipid interactions that confer to the tail tube elastic, mechanical and functional properties employed also in other protein-membrane systems.
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Affiliation(s)
- Bibiana Peralta
- Structural Biology Unit, CIC bioGUNE, CIBERehd, Derio, Spain
| | | | - Daniel Castaño-Díez
- Center for Cellular Imaging and Nano-Analitics (C-CINA) Biozentrum, University of Basel, Basel, Switzerland
| | - Aurelie Bertin
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université de Paris–Sud, Orsay, France
| | - Claire Boulogne
- Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Université de Paris–Sud, Orsay, France
| | - Hanna M. Oksanen
- Institute of Biotechnology and Department of Biosciences, Viikki Biocenter, University of Helsinki, Finland
| | - Dennis H. Bamford
- Institute of Biotechnology and Department of Biosciences, Viikki Biocenter, University of Helsinki, Finland
| | - Nicola G. A. Abrescia
- Structural Biology Unit, CIC bioGUNE, CIBERehd, Derio, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- * E-mail:
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Calcium ion-dependent entry of the membrane-containing bacteriophage PM2 into its Pseudoalteromonas host. Virology 2010; 405:120-8. [PMID: 20646729 DOI: 10.1016/j.virol.2010.05.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Revised: 05/09/2010] [Accepted: 05/19/2010] [Indexed: 11/22/2022]
Abstract
Marine bacteriophage PM2 infects gram-negative Pseudoalteromonas species and is currently the only assigned member of the Corticoviridae family. The icosahedral protein shell covers an internal protein-rich phage membrane that encloses the highly supercoiled dsDNA genome. In this study we investigated PM2 entry into the host. Our results indicate that PM2 adsorption to the host is dependent on the intracellular ATP concentration, while genome penetration through the cytoplasmic membrane depends on the presence of millimolar concentrations of calcium ions in the medium. In the absence of Ca(2+) the infection is arrested at the entry stage but can be rescued by the addition of Ca(2+). Interestingly, PM2 entry induces abrupt cell lysis if the host outer membrane is not stabilized by divalent cations. Experimental data described in this study in combination with results obtained previously allowed us to propose a sequential model describing the entry of bacteriophage PM2 into the host cells.
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Abrescia NGA, Cockburn JJB, Grimes JM, Sutton GC, Diprose JM, Butcher SJ, Fuller SD, San Martín C, Burnett RM, Stuart DI, Bamford DH, Bamford JKH. Insights into assembly from structural analysis of bacteriophage PRD1. Nature 2004; 432:68-74. [PMID: 15525981 DOI: 10.1038/nature03056] [Citation(s) in RCA: 201] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2004] [Accepted: 09/21/2004] [Indexed: 11/09/2022]
Abstract
The structure of the membrane-containing bacteriophage PRD1 has been determined by X-ray crystallography at about 4 A resolution. Here we describe the structure and location of proteins P3, P16, P30 and P31. Different structural proteins seem to have specialist roles in controlling virus assembly. The linearly extended P30 appears to nucleate the formation of the icosahedral facets (composed of trimers of the major capsid protein, P3) and acts as a molecular tape-measure, defining the size of the virus and cementing the facets together. Pentamers of P31 form the vertex base, interlocking with subunits of P3 and interacting with the membrane protein P16. The architectural similarities with adenovirus and one of the largest known virus particles PBCV-1 support the notion that the mechanism of assembly of PRD1 is scaleable and applies across the major viral lineage formed by these viruses.
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Affiliation(s)
- Nicola G A Abrescia
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7BN, UK
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Jaatinen ST, Viitanen SJ, Bamford DH, Bamford JKH. Integral membrane protein P16 of bacteriophage PRD1 stabilizes the adsorption vertex structure. J Virol 2004; 78:9790-7. [PMID: 15331712 PMCID: PMC514979 DOI: 10.1128/jvi.78.18.9790-9797.2004] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The icosahedral membrane-containing double-stranded DNA bacteriophage PRD1 has a labile receptor binding spike complex at the vertices. This complex, which is analogous to that of adenovirus, is formed of the penton protein P31, the spike protein P5, and the receptor binding protein P2. Upon infection, the internal phage membrane transforms into a tubular structure that protrudes through a vertex and penetrates the cell envelope for DNA injection. We describe here a new class of PRD1 mutants lacking virion-associated integral membrane protein P16. P16 links the spike complex to the viral membrane and is necessary for spike stability. We also show that the unique vertex used for DNA packaging is intact in the P16-deficient particle, indicating that the 11 adsorption vertices and the 1 portal vertex are functionally and structurally distinct.
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Affiliation(s)
- Silja T Jaatinen
- Viikki Biocenter 2, P.O. Box 56 (Viikinkaari 5), FIN-00014 University of Helsinki, Finland
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Ravantti JJ, Gaidelyte A, Bamford DH, Bamford JKH. Comparative analysis of bacterial viruses Bam35, infecting a gram-positive host, and PRD1, infecting gram-negative hosts, demonstrates a viral lineage. Virology 2003; 313:401-14. [PMID: 12954208 DOI: 10.1016/s0042-6822(03)00295-2] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Extra- and intracellular viruses in the biosphere outnumber their cellular hosts by at least one order of magnitude. How is this enormous domain of viruses organized? Sampling of the virosphere has been scarce and focused on viruses infecting humans, cultivated plants, and animals as well as those infecting well-studied bacteria. It has been relatively easy to cluster closely related viruses based on their genome sequences. However, it has been impossible to establish long-range evolutionary relationships as sequence homology diminishes. Recent advances in the evaluation of virus architecture by high-resolution structural analysis and elucidation of viral functions have allowed new opportunities for establishment of possible long-range phylogenic relationships-virus lineages. Here, we use a genomic approach to investigate a proposed virus lineage formed by bacteriophage PRD1, infecting gram-negative bacteria, and human adenovirus. The new member of this proposed lineage, bacteriophage Bam35, is morphologically indistinguishable from PRD1. It infects gram-positive hosts that evolutionarily separated from gram-negative bacteria more than one billion years ago. For example, it can be inferred from structural analysis of the coat protein sequence that the fold is very similar to that of PRD1. This and other observations made here support the idea that a common early ancestor for Bam35, PRD1, and adenoviruses existed.
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Affiliation(s)
- Janne J Ravantti
- Department of Computer Science, P.O. Box 26, (Teollisuuskatu 23), 00014 University of Helsinki, Helsinki, Finland
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Gowen B, Bamford JKH, Bamford DH, Fuller SD. The tailless icosahedral membrane virus PRD1 localizes the proteins involved in genome packaging and injection at a unique vertex. J Virol 2003; 77:7863-71. [PMID: 12829826 PMCID: PMC161952 DOI: 10.1128/jvi.77.14.7863-7871.2003] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The double-stranded DNA (dsDNA) virus PRD1 carries its genome in a membrane surrounded by an icosahedral protein shell. The shell contains 240 copies of the trimeric P3 protein arranged with a pseudo T = 25 triangulation that is reminiscent of the mammalian adenovirus. DNA packaging and infection are believed to occur through the vertices of the particle. We have used immunolabeling to define the distribution of proteins on the virion surface. Antibodies to protein P3 labeled the entire surface of the virus. Most of the 12 vertices labeled with antibodies directed against proteins P5, P2, and P31. These proteins are known to function in virus binding to the cell surface. Proteins P6, P11, and P20 were found on a single vertex per virion. The P6 and P20 proteins are believed to function in DNA packaging. Protein P11 is a pilot protein that is involved in a complex that mediates the early stages of DNA entry to the host cell. Labeling with antibodies to P5 or P2 did not affect the labeling of P6, the unique vertex protein. Labeling with antibodies to the unique vertex protein P6 interfered with the labeling by antibodies to the unique vertex protein P20. We conclude that PRD1 utilizes 11 of its vertices for initial receptor binding. It utilizes a single, unique vertex for both DNA packing during assembly and DNA delivery during infection.
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Affiliation(s)
- Brent Gowen
- The Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Henry Wellcome Building for Genomic Medicine, University of Oxford, Headington, Oxford OX3 7BN, United Kingdom
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Huiskonen JT, Laakkonen L, Toropainen M, Sarvas M, Bamford DH, Bamford JKH. Probing the ability of the coat and vertex protein of the membrane-containing bacteriophage PRD1 to display a meningococcal epitope. Virology 2003; 310:267-79. [PMID: 12781714 DOI: 10.1016/s0042-6822(03)00171-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Bacteriophage PRD1 is an icosahedral dsDNA virus with a diameter of 740 A and an outer protein shell composed of 720 copies of major coat protein P3. Spike complexes at the vertices are composed of a pentameric base (protein P31) and a spike structure (proteins P5 and P2) where the N-terminal region of the trimeric P5 is associated with the base and the C-terminal region of P5 is associated with receptor-binding protein P2. The functionality of proteins P3 and P5 was investigated using insertions and deletions. It was observed that P3 did not tolerate changes whereas P5 tolerated changes much more freely. These properties support the hypothesis that viruses have core structures and functions, which remain stable over time, as well as other elements, responsible for host interactions, which are evolutionally more fluid. The insertional probe used was the apex of exposed loop 4 of group B meningococcal outer membrane protein PorA, a medically important subunit vaccine candidate. It was demonstrated that the epitope could be displayed on the virus surface as part of spike protein P5.
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Affiliation(s)
- Juha T Huiskonen
- Department of Biosciences and Institute of Biotechnology, University of Helsinki, Finland
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Strömsten NJ, Bamford DH, Bamford JKH. The unique vertex of bacterial virus PRD1 is connected to the viral internal membrane. J Virol 2003; 77:6314-21. [PMID: 12743288 PMCID: PMC155016 DOI: 10.1128/jvi.77.11.6314-6321.2003] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Icosahedral double-stranded DNA (dsDNA) bacterial viruses are known to package their genomes into preformed procapsids via a unique portal vertex. Bacteriophage PRD1 differs from the more commonly known icosahedral dsDNA phages in that it contains an internal lipid membrane. The packaging of PRD1 is known to proceed via preformed empty capsids. Now, a unique vertex has been shown to exist in PRD1. We show in this study that this unique vertex extends to the virus internal membrane via two integral membrane proteins, P20 and P22. These small membrane proteins are necessary for the binding of the putative packaging ATPase P9, via another capsid protein, P6, to the virus particle.
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Affiliation(s)
- Nelli J Strömsten
- Department of Biosciences and Institute of Biotechnology, Biocenter 2, FIN-00014 University of Helsinki, Finland
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Grahn AM, Daugelavicius R, Bamford DH. Sequential model of phage PRD1 DNA delivery: active involvement of the viral membrane. Mol Microbiol 2002; 46:1199-209. [PMID: 12453208 DOI: 10.1046/j.1365-2958.2002.03250.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
DNA translocation across the barriers of recipient cells is not well understood. Viral DNA delivery mechanisms offer an opportunity to obtain useful information in systems in which the process can be arrested to a number of stages. PRD1 is an icosahedral double-stranded (ds)DNA bacterial virus with an internal membrane. It is an atypical dsDNA phage, as any of the vertex spikes can be used for receptor recognition. In this report, we dissect the PRD1 DNA entry into a number of steps: (i) outer membrane (OM) penetration; (ii) peptidoglycan digestion; (iii) cytoplasmic membrane (CM) penetration; and (iv) DNA translocation. We present a model for PRD1 DNA entry proposing that the initial stage of entry is powered by the pressure build-up during DNA packaging. The viral protein P11 is shown to function as the first DNA delivery protein needed to penetrate the OM. We also report a DNA translocation machinery composed of at least three viral integral membrane proteins, P14, P18 and P32.
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Affiliation(s)
- A Marika Grahn
- Department of Biosciences and Institute of Biotechnology, University of Helsinki, Finland
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Bamford JKH, Cockburn JJB, Diprose J, Grimes JM, Sutton G, Stuart DI, Bamford DH. Diffraction quality crystals of PRD1, a 66-MDa dsDNA virus with an internal membrane. J Struct Biol 2002; 139:103-12. [PMID: 12406692 DOI: 10.1016/s1047-8477(02)00562-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
It has proved difficult to obtain well diffracting single crystals of macromolecular complexes rich in lipid. We report here the path that has led to crystals of the bacteriophage PRD1, a particle containing approximately 2,000 protein subunits from 18 different protein species, around 10 of which are integral membrane proteins associated with a host-derived lipid bilayer of some 12,500 lipid molecules. These crystals are capable of diffracting X-rays to Bragg spacings below 4A. It is hoped that some lessons learned from PRD1 will be applicable to other lipidic systems and that these crystals will allow, as a proof of principle, the determination of the structure of the virus in terms of a detailed atomic model.
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Affiliation(s)
- Jaana K H Bamford
- Institute of Biotechnology and Department of Biosciences, Biocenter 2, University of Helsinki, P.O. Box 56, Viikinkaari 5, 00014 University of Helsinki, Finland.
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