1
|
Fàbrega-Ferrer M, Cuervo A, Fernández FJ, Machón C, Pérez-Luque R, Pous J, Vega MC, Carrascosa JL, Coll M. Using a partial atomic model from medium-resolution cryo-EM to solve a large crystal structure. Acta Crystallogr D Struct Biol 2021; 77:11-18. [PMID: 33404521 PMCID: PMC7787105 DOI: 10.1107/s2059798320015156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 11/13/2020] [Indexed: 11/21/2022] Open
Abstract
Medium-resolution cryo-electron microscopy maps, in particular when they include a significant number of α-helices, may allow the building of partial models that are useful for molecular-replacement searches in large crystallographic structures when the structures of homologs are not available and experimental phasing has failed. Here, as an example, the solution of the structure of a bacteriophage portal using a partial 30% model built into a 7.8 Å resolution cryo-EM map is shown. Inspection of the self-rotation function allowed the correct oligomerization state to be determined, and density-modification procedures using rotation matrices and a mask based on the cryo-EM structure were critical for solving the structure. A workflow is described that may be applicable to similar cases and this strategy is compared with direct use of the cryo-EM map for molecular replacement.
Collapse
Affiliation(s)
- Montserrat Fàbrega-Ferrer
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
- Institut de Biologia Molecular de Barcelona (IBMB–CSIC), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Ana Cuervo
- Centro Nacional de Biotecnología (CNB–CSIC), Darwin 3, 28049 Madrid, Spain
| | - Francisco J. Fernández
- Centro de Investigaciones Biológicas (CIB–CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Cristina Machón
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
- Institut de Biologia Molecular de Barcelona (IBMB–CSIC), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Rosa Pérez-Luque
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
- Institut de Biologia Molecular de Barcelona (IBMB–CSIC), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Joan Pous
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - M. Cristina Vega
- Centro de Investigaciones Biológicas (CIB–CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - José L. Carrascosa
- Centro Nacional de Biotecnología (CNB–CSIC), Darwin 3, 28049 Madrid, Spain
| | - Miquel Coll
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
- Institut de Biologia Molecular de Barcelona (IBMB–CSIC), Baldiri Reixac 10, 08028 Barcelona, Spain
| |
Collapse
|
2
|
Zeng L, Ding W, Hao Q. Using cryo-electron microscopy maps for X-ray structure determination. IUCRJ 2018; 5:382-389. [PMID: 30002839 PMCID: PMC6038958 DOI: 10.1107/s2052252518005857] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 04/16/2018] [Indexed: 06/08/2023]
Abstract
X-ray crystallography and cryo-electron microscopy (cryo-EM) are complementary techniques for structure determination. Crystallography usually reveals more detailed information, while cryo-EM is an extremely useful technique for studying large-sized macromolecules. As the gap between the resolution of crystallography and cryo-EM data narrows, the cryo-EM map of a macromolecule could serve as an initial model to solve the phase problem of crystal diffraction for high-resolution structure determination. FSEARCH is a procedure to utilize the low-resolution molecular shape for crystallographic phasing. The IPCAS (Iterative Protein Crystal structure Automatic Solution) pipeline is an automatic direct-methods-aided dual-space iterative phasing and model-building procedure. When only an electron-density map is available as the starting point, IPCAS is capable of generating a completed model from the phases of the input map automatically, without the requirement of an initial model. In this study, a hybrid method integrating X-ray crystallography with cryo-EM to help with structure determination is presented. With a cryo-EM map as the starting point, the workflow of the method involves three steps. (1) Cryo-EM map replacement: FSEARCH is utilized to find the correct translation and orientation of the cryo-EM map in the crystallographic unit cell and generates the initial low-resolution map. (2) Phase extension: the phases calculated from the correctly placed cryo-EM map are extended to high-resolution X-ray data by non-crystallographic symmetry averaging with phenix.resolve. (3) Model building: IPCAS is used to generate an initial model using the phase-extended map and perform model completion by iteration. Four cases (the lowest cryo-EM map resolution being 6.9 Å) have been tested for the general applicability of the hybrid method, and almost complete models have been generated for all test cases with reasonable Rwork/Rfree. The hybrid method therefore provides an automated tool for X-ray structure determination using a cryo-EM map as the starting point.
Collapse
Affiliation(s)
- Lingxiao Zeng
- School of Biomedical Sciences, University of Hong Kong, 21 Sassoon Road, Hong Kong
| | - Wei Ding
- Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
| | - Quan Hao
- School of Biomedical Sciences, University of Hong Kong, 21 Sassoon Road, Hong Kong
- Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
| |
Collapse
|
3
|
Wang J, Wang W, Song W, Han Z, Zhang H, Chai J, Wang H, Wang J. An improved method for phasing crystal structures with low non-crystallographic symmetry using cryo-electron microscopy data. Protein Cell 2016; 6:919-23. [PMID: 26507843 PMCID: PMC4656207 DOI: 10.1007/s13238-015-0219-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Jia Wang
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Weiguang Wang
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Wen Song
- Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Ministry of Education Key Laboratory of Protein Science, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Zhifu Han
- Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Ministry of Education Key Laboratory of Protein Science, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Heqiao Zhang
- Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Ministry of Education Key Laboratory of Protein Science, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jijie Chai
- Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China. .,Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China. .,Ministry of Education Key Laboratory of Protein Science, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Hongwei Wang
- Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China. .,Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China. .,Ministry of Education Key Laboratory of Protein Science, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Jiawei Wang
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China. .,Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| |
Collapse
|
4
|
Wang J, Chai J, Wang H. Structure of the mouse Toll-like receptor 13 ectodomain in complex with a conserved sequence from bacterial 23S ribosomal RNA. FEBS J 2016; 283:1631-5. [PMID: 26676765 DOI: 10.1111/febs.13628] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 12/09/2015] [Accepted: 12/11/2015] [Indexed: 11/30/2022]
Abstract
Toll-like receptor 13 (TLR13) recognizes a conserved 10-nucleotide sequence from bacterial 23S ribosomal RNA, and binding of TLR13 to the target rRNA molecule triggers immune responses. Recently, the crystal structure of the TLR13 ectodomain bound by a 13-nucleotide single-stranded RNA (ssRNA13) was determined by using the initial phases provided by a cryo-electron microscopy map of TLR13 in complex with a 25-nucleotide ssRNA (ssRNA25). This structural snapshot describes a unique method for solving the crystal structure of the TLR13-ssRNA13 complex based on medium-resolution reconstruction of TLR13-ssRNA25 cryo-electron microscopy images.
Collapse
Affiliation(s)
- Jiawei Wang
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jijie Chai
- Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.,Ministry of Education Key Laboratory of Protein Science, School of Life Sciences, Tsinghua University, Beijing, China
| | - Hongwei Wang
- Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.,Ministry of Education Key Laboratory of Protein Science, School of Life Sciences, Tsinghua University, Beijing, China
| |
Collapse
|
5
|
X-ray structure determination using low-resolution electron microscopy maps for molecular replacement. Nat Protoc 2015; 10:1275-84. [PMID: 26226459 DOI: 10.1038/nprot.2015.069] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Structures of multisubunit macromolecular machines are primarily determined either by electron microscopy (EM) or by X-ray crystallography. In many cases, a structure for a complex can be obtained at low resolution (at a coarse level of detail) with EM and at a higher resolution (with finer detail) by X-ray crystallography. The integration of these two structural techniques is becoming increasingly important for the generation of atomic models of macromolecular complexes. A low-resolution EM image can be a powerful tool for obtaining the 'phase' information that is missing from an X-ray crystallography experiment; however, integration of EM and X-ray diffraction data has been technically challenging. Here we present a step-by-step protocol that explains how low-resolution EM maps can be placed in the crystallographic unit cell by molecular replacement, and how initial phases computed from the placed EM density are extended to high resolution by averaging maps over noncrystallographic symmetry. As the resolution gap between EM and X-ray crystallography continues to narrow, the use of EM maps to help with X-ray crystal structure determination, as described in this protocol, will become increasingly effective.
Collapse
|
6
|
Zheng H, Handing KB, Zimmerman MD, Shabalin IG, Almo SC, Minor W. X-ray crystallography over the past decade for novel drug discovery - where are we heading next? Expert Opin Drug Discov 2015; 10:975-89. [PMID: 26177814 DOI: 10.1517/17460441.2015.1061991] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Macromolecular X-ray crystallography has been the primary methodology for determining the three-dimensional structures of proteins, nucleic acids and viruses. Structural information has paved the way for structure-guided drug discovery and laid the foundations for structural bioinformatics. However, X-ray crystallography still has a few fundamental limitations, some of which may be overcome and complemented using emerging methods and technologies in other areas of structural biology. AREAS COVERED This review describes how structural knowledge gained from X-ray crystallography has been used to advance other biophysical methods for structure determination (and vice versa). This article also covers current practices for integrating data generated by other biochemical and biophysical methods with those obtained from X-ray crystallography. Finally, the authors articulate their vision about how a combination of structural and biochemical/biophysical methods may improve our understanding of biological processes and interactions. EXPERT OPINION X-ray crystallography has been, and will continue to serve as, the central source of experimental structural biology data used in the discovery of new drugs. However, other structural biology techniques are useful not only to overcome the major limitation of X-ray crystallography, but also to provide complementary structural data that is useful in drug discovery. The use of recent advancements in biochemical, spectroscopy and bioinformatics methods may revolutionize drug discovery, albeit only when these data are combined and analyzed with effective data management systems. Accurate and complete data management is crucial for developing experimental procedures that are robust and reproducible.
Collapse
Affiliation(s)
- Heping Zheng
- University of Virginia, Department of Molecular Physiology and Biological Physics , 1340 Jefferson Park Avenue, Charlottesville, VA 22908 , USA +1 434 243 6865 ; +1 434 243 2981 ;
| | | | | | | | | | | |
Collapse
|
7
|
Lo VL, Kingston RL, Millane RP. Iterative projection algorithms in protein crystallography. II. Application. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2015; 71:451-9. [PMID: 26131900 DOI: 10.1107/s2053273315005574] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 03/18/2015] [Indexed: 11/10/2022]
Abstract
Iterative projection algorithms (IPAs) are a promising tool for protein crystallographic phase determination. Although related to traditional density-modification algorithms, IPAs have better convergence properties, and, as a result, can effectively overcome the phase problem given modest levels of structural redundancy. This is illustrated by applying IPAs to determine the electron densities of two protein crystals with fourfold non-crystallographic symmetry, starting with only the experimental diffraction amplitudes, a low-resolution molecular envelope and the position of the non-crystallographic axes. The algorithm returns electron densities that are sufficiently accurate for model building, allowing automated recovery of the known structures. This study indicates that IPAs should find routine application in protein crystallography, being capable of reconstructing electron densities starting with very little initial phase information.
Collapse
Affiliation(s)
- Victor L Lo
- Computational Imaging Group, Department of Electrical and Computer Engineering, University of Canterbury, Christchurch, New Zealand
| | - Richard L Kingston
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Rick P Millane
- Computational Imaging Group, Department of Electrical and Computer Engineering, University of Canterbury, Christchurch, New Zealand
| |
Collapse
|
8
|
Moreno-Morcillo M, Taylor NMI, Gruene T, Legrand P, Rashid UJ, Ruiz FM, Steuerwald U, Müller CW, Fernández-Tornero C. Solving the RNA polymerase I structural puzzle. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2570-82. [PMID: 25286842 PMCID: PMC4188003 DOI: 10.1107/s1399004714015788] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 07/06/2014] [Indexed: 11/28/2022]
Abstract
Knowing the structure of multi-subunit complexes is critical to understand basic cellular functions. However, when crystals of these complexes can be obtained they rarely diffract beyond 3 Å resolution, which complicates X-ray structure determination and refinement. The crystal structure of RNA polymerase I, an essential cellular machine that synthesizes the precursor of ribosomal RNA in the nucleolus of eukaryotic cells, has recently been solved. Here, the crucial steps that were undertaken to build the atomic model of this multi-subunit enzyme are reported, emphasizing how simple crystallographic experiments can be used to extract relevant biological information. In particular, this report discusses the combination of poor molecular replacement and experimental phases, the application of multi-crystal averaging and the use of anomalous scatterers as sequence markers to guide tracing and to locate the active site. The methods outlined here will likely serve as a reference for future structural determination of large complexes at low resolution.
Collapse
Affiliation(s)
- María Moreno-Morcillo
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Nicholas M. I. Taylor
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Tim Gruene
- Department of Structural Chemistry, Georg-August-University, Tammannstrasse 4, 37077 Göttingen, Germany
| | - Pierre Legrand
- SOLEIL Synchrotron, L’Orme de Merisiers, Saint Aubin, Gif-sur-Yvette, France
| | - Umar J. Rashid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Federico M. Ruiz
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Ulrich Steuerwald
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Christoph W. Müller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Carlos Fernández-Tornero
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| |
Collapse
|
9
|
Zhao H, Sheng G, Wang J, Wang M, Bunkoczi G, Gong W, Wei Z, Wang Y. Crystal structure of the RNA-guided immune surveillance Cascade complex in Escherichia coli. Nature 2014; 515:147-50. [DOI: 10.1038/nature13733] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 08/05/2014] [Indexed: 12/18/2022]
|
10
|
Shi D, Nannenga BL, Iadanza MG, Gonen T. Three-dimensional electron crystallography of protein microcrystals. eLife 2013; 2:e01345. [PMID: 24252878 PMCID: PMC3831942 DOI: 10.7554/elife.01345] [Citation(s) in RCA: 265] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We demonstrate that it is feasible to determine high-resolution protein structures by electron crystallography of three-dimensional crystals in an electron cryo-microscope (CryoEM). Lysozyme microcrystals were frozen on an electron microscopy grid, and electron diffraction data collected to 1.7 Å resolution. We developed a data collection protocol to collect a full-tilt series in electron diffraction to atomic resolution. A single tilt series contains up to 90 individual diffraction patterns collected from a single crystal with tilt angle increment of 0.1–1° and a total accumulated electron dose less than 10 electrons per angstrom squared. We indexed the data from three crystals and used them for structure determination of lysozyme by molecular replacement followed by crystallographic refinement to 2.9 Å resolution. This proof of principle paves the way for the implementation of a new technique, which we name ‘MicroED’, that may have wide applicability in structural biology. DOI:http://dx.doi.org/10.7554/eLife.01345.001 X-ray crystallography has been used to work out the atomic structure of a large number of proteins. In a typical X-ray crystallography experiment, a beam of X-rays is directed at a protein crystal, which scatters some of the X-ray photons to produce a diffraction pattern. The crystal is then rotated through a small angle and another diffraction pattern is recorded. Finally, after this process has been repeated enough times, it is possible to work backwards from the diffraction patterns to figure out the structure of the protein. The crystals used for X-ray crystallography must be large to withstand the damage caused by repeated exposure to the X-ray beam. However, some proteins do not form crystals at all, and others only form small crystals. It is possible to overcome this problem by using extremely short pulses of X-rays, but this requires a very large number of small crystals and ultrashort X-ray pulses are only available at a handful of research centers around the world. There is, therefore, a need for other approaches that can determine the structure of proteins that only form small crystals. Electron crystallography is similar to X-ray crystallography in that a protein crystal scatters a beam to produce a diffraction pattern. However, the interactions between the electrons in the beam and the crystal are much stronger than those between the X-ray photons and the crystal. This means that meaningful amounts of data can be collected from much smaller crystals. However, it is normally only possible to collect one diffraction pattern from each crystal because of beam induced damage. Researchers have developed methods to merge the diffraction patterns produced by hundreds of small crystals, but to date these techniques have only worked with very thin two-dimensional crystals that contain only one layer of the protein of interest. Now Shi et al. report a new approach to electron crystallography that works with very small three-dimensional crystals. Called MicroED, this technique involves placing the crystal in a transmission electron cryo-microscope, which is a fairly standard piece of equipment in many laboratories. The normal ‘low-dose’ electron beam in one of these microscopes would normally damage the crystal after a single diffraction pattern had been collected. However, Shi et al. realized that it was possible to obtain diffraction patterns without severely damaging the crystal if they dramatically reduced the normal low-dose electron beam. By reducing the electron dose by a factor of 200, it was possible to collect up to 90 diffraction patterns from the same, very small, three-dimensional crystal, and then—similar to what happens in X-ray crystallography—work backwards to figure out the structure of the protein. Shi et al. demonstrated the feasibility of the MicroED approach by using it to determine the structure of lysozyme, which is widely used as a test protein in crystallography, with a resolution of 2.9 Å. This proof-of principle study paves the way for crystallographers to study protein that cannot be studied with existing techniques. DOI:http://dx.doi.org/10.7554/eLife.01345.002
Collapse
Affiliation(s)
- Dan Shi
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | | | | | | |
Collapse
|
11
|
Scapin G. Molecular replacement then and now. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2266-75. [PMID: 24189239 PMCID: PMC3817701 DOI: 10.1107/s0907444913011426] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 04/26/2013] [Indexed: 01/22/2023]
Abstract
The `phase problem' in crystallography results from the inability to directly measure the phases of individual diffracted X-ray waves. While intensities are directly measured during data collection, phases must be obtained by other means. Several phasing methods are available (MIR, SAR, MAD, SAD and MR) and they all rely on the premise that phase information can be obtained if the positions of marker atoms in the unknown crystal structure are known. This paper is dedicated to the most popular phasing method, molecular replacement (MR), and represents a personal overview of the development, use and requirements of the methodology. The first description of noncrystallographic symmetry as a tool for structure determination was explained by Rossmann and Blow [Rossmann & Blow (1962), Acta Cryst. 15, 24-31]. The term `molecular replacement' was introduced as the name of a book in which the early papers were collected and briefly reviewed [Rossmann (1972), The Molecular Replacement Method. New York: Gordon & Breach]. Several programs have evolved from the original concept to allow faster and more sophisticated searches, including six-dimensional searches and brute-force approaches. While careful selection of the resolution range for the search and the quality of the data will greatly influence the outcome, the correct choice of the search model is probably still the main criterion to guarantee success in solving a structure using MR. Two of the main parameters used to define the `best' search model are sequence identity (25% or more) and structural similarity. Another parameter that may often be undervalued is the quality of the probe: there is clearly a relationship between the quality and the correctness of the chosen probe and its usefulness as a search model. Efforts should be made by all structural biologists to ensure that their deposited structures, which are potential search probes for future systems, are of the best possible quality.
Collapse
Affiliation(s)
- Giovanna Scapin
- Global Structural Chemistry, Merck and Co. Inc, 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA
| |
Collapse
|
12
|
Stuart DI, Abrescia NGA. From lows to highs: using low-resolution models to phase X-ray data. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2257-65. [PMID: 24189238 PMCID: PMC3817700 DOI: 10.1107/s0907444913022336] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 08/08/2013] [Indexed: 11/11/2022]
Abstract
The study of virus structures has contributed to methodological advances in structural biology that are generally applicable (molecular replacement and noncrystallographic symmetry are just two of the best known examples). Moreover, structural virology has been instrumental in forging the more general concept of exploiting phase information derived from multiple structural techniques. This hybridization of structural methods, primarily electron microscopy (EM) and X-ray crystallography, but also small-angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) spectroscopy, is central to integrative structural biology. Here, the interplay of X-ray crystallography and EM is illustrated through the example of the structural determination of the marine lipid-containing bacteriophage PM2. Molecular replacement starting from an ~13 Å cryo-EM reconstruction, followed by cycling density averaging, phase extension and solvent flattening, gave the X-ray structure of the intact virus at 7 Å resolution This in turn served as a bridge to phase, to 2.5 Å resolution, data from twinned crystals of the major coat protein (P2), ultimately yielding a quasi-atomic model of the particle, which provided significant insights into virus evolution and viral membrane biogenesis.
Collapse
Affiliation(s)
- David I. Stuart
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7BN, England
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, England
| | - Nicola G. A. Abrescia
- Structural Biology Unit, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, Bld 800, 48160 Derio, Spain
- IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
| |
Collapse
|
13
|
Abstract
Three-dimensional (3D) cryoelectron microscopy reconstruction methods are uniquely able to reveal structures of many important macromolecules and macromolecular complexes. EMDataBank.org, a joint effort of the Protein Databank in Europe (PDBe), the Research Collaboratory for Structural Bioinformatics (RCSB), and the National Center for Macromolecular Imaging (NCMI), is a "one-stop shop" resource for global deposition and retrieval of cryo-EM map, model, and associated metadata. The resource unifies public access to the two major EM Structural Data archives: EM Data Bank (EMDB) and Protein Data Bank (PDB), and facilitates use of EM structural data of macromolecules and macromolecular complexes by the wider scientific community.
Collapse
Affiliation(s)
- Catherine L Lawson
- Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, USA
| |
Collapse
|
14
|
Lawson CL, Baker ML, Best C, Bi C, Dougherty M, Feng P, van Ginkel G, Devkota B, Lagerstedt I, Ludtke SJ, Newman RH, Oldfield TJ, Rees I, Sahni G, Sala R, Velankar S, Warren J, Westbrook JD, Henrick K, Kleywegt GJ, Berman HM, Chiu W. EMDataBank.org: unified data resource for CryoEM. Nucleic Acids Res 2010; 39:D456-64. [PMID: 20935055 PMCID: PMC3013769 DOI: 10.1093/nar/gkq880] [Citation(s) in RCA: 195] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Cryo-electron microscopy reconstruction methods are uniquely able to reveal structures of many important macromolecules and macromolecular complexes. EMDataBank.org, a joint effort of the Protein Data Bank in Europe (PDBe), the Research Collaboratory for Structural Bioinformatics (RCSB) and the National Center for Macromolecular Imaging (NCMI), is a global ‘one-stop shop’ resource for deposition and retrieval of cryoEM maps, models and associated metadata. The resource unifies public access to the two major archives containing EM-based structural data: EM Data Bank (EMDB) and Protein Data Bank (PDB), and facilitates use of EM structural data of macromolecules and macromolecular complexes by the wider scientific community.
Collapse
Affiliation(s)
- Catherine L Lawson
- Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 610 Taylor Road Piscataway, NJ 08854, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Abstract
In all organisms, fatty acid synthesis is achieved in variations of a common cyclic reaction pathway by stepwise, iterative elongation of precursors with two-carbon extender units. In bacteria, all individual reaction steps are carried out by monofunctional dissociated enzymes, whereas in eukaryotes the fatty acid synthases (FASs) have evolved into large multifunctional enzymes that integrate the whole process of fatty acid synthesis. During the last few years, important advances in understanding the structural and functional organization of eukaryotic FASs have been made through a combination of biochemical, electron microscopic and X-ray crystallographic approaches. They have revealed the strikingly different architectures of the two distinct types of eukaryotic FASs, the fungal and the animal enzyme system. Fungal FAS is a 2·6 MDa α₆β₆ heterododecamer with a barrel shape enclosing two large chambers, each containing three sets of active sites separated by a central wheel-like structure. It represents a highly specialized micro-compartment strictly optimized for the production of saturated fatty acids. In contrast, the animal FAS is a 540 kDa X-shaped homodimer with two lateral reaction clefts characterized by a modular domain architecture and large extent of conformational flexibility that appears to contribute to catalytic efficiency.
Collapse
|
16
|
Heuser P, Langer GG, Lamzin VS. Interpretation of very low resolution X-ray electron-density maps using core objects. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:690-6. [PMID: 19564689 PMCID: PMC2703575 DOI: 10.1107/s090744490901991x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2009] [Accepted: 05/25/2009] [Indexed: 11/11/2022]
Abstract
A novel approach to obtaining structural information from macromolecular X-ray data extending to resolutions as low as 20 A is presented. Following a simple map-segmentation procedure, the approximate shapes of the domains forming the structure are identified. A pattern-recognition comparative analysis of these shapes and those derived from the structures of domains from the PDB results in candidate structural models that can be used for a fit into the density map. It is shown that the placed candidate models can be employed for subsequent phase extension to higher resolution.
Collapse
Affiliation(s)
- Philipp Heuser
- Hamburg Unit, European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, Hamburg 22603, Germany.
| | | | | |
Collapse
|
17
|
Jenni S, Ban N. Imperfect pseudo-merohedral twinning in crystals of fungal fatty acid synthase. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:101-11. [PMID: 19171964 PMCID: PMC2631638 DOI: 10.1107/s0907444909000778] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2008] [Accepted: 01/07/2009] [Indexed: 11/23/2022]
Abstract
A case of imperfect pseudo-merohedral twinning in monoclinic crystals of fungal fatty acid synthase is discussed. A space-group transition during crystal dehydration resulted in a Moiré pattern-like interference of the twinned diffraction patterns. The recent high-resolution structures of fungal fatty acid synthase (FAS) have provided new insights into the principles of fatty acid biosynthesis by large multifunctional enzymes. The crystallographic phase problem for the 2.6 MDa fungal FAS was initially solved to 5 Å resolution using two crystal forms from Thermomyces lanuginosus. Monoclinic crystals in space group P21 were obtained from orthorhombic crystals in space group P212121 by dehydration. Here, it is shown how this space-group transition induced imperfect pseudo-merohedral twinning in the monoclinic crystal, giving rise to a Moiré pattern-like interference of the two twin-related reciprocal lattices. The strategy for processing the twinned diffraction images and obtaining a quantitative analysis is presented. The twinning is also related to the packing of the molecules in the two crystal forms, which was derived from self-rotation function analysis and molecular-replacement solutions using a low-resolution electron microscopy map as a search model.
Collapse
Affiliation(s)
- Simon Jenni
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.
| | | |
Collapse
|