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Obita T, Inaka K, Kohda D, Maita N. Crystal structure of the PX domain of Vps17p from Saccharomyces cerevisiae. Acta Crystallogr F Struct Biol Commun 2022; 78:210-216. [PMID: 35506766 PMCID: PMC9067373 DOI: 10.1107/s2053230x22004472] [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: 03/24/2022] [Accepted: 04/27/2022] [Indexed: 11/10/2022] Open
Abstract
The structure determination of the PX (phox homology) domain of the Saccharomyces cerevisiae Vps17p protein presented a challenging case for molecular replacement because it has noncrystallographic symmetry close to a crystallographic axis. The combination of diffraction-quality crystals grown under microgravity on the International Space Station and a highly accurate template structure predicted by AlphaFold2 provided the key to successful crystal structure determination. Although the structure of the Vps17p PX domain is seen in many PX domains, no basic residues are found around the canonical phosphatidylinositol phosphate (PtdIns-P) binding site, suggesting an inability to bind PtdIns-P molecules.
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Affiliation(s)
- Takayuki Obita
- Faculty of Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Koji Inaka
- Maruwa Foods and Biosciences Inc., Yamatokoriyama, Nara 639-1123, Japan
| | - Daisuke Kohda
- Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Nobuo Maita
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba 263-8555, Japan
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2
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Wang J, Gisriel CJ, Reiss K, Huang HL, Armstrong WH, Brudvig GW, Batista VS. Heterogeneous Composition of Oxygen-Evolving Complexes in Crystal Structures of Dark-Adapted Photosystem II. Biochemistry 2021; 60:3374-3384. [PMID: 34714055 DOI: 10.1021/acs.biochem.1c00611] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photosystem II (PSII) is a homodimeric protein complex that catalyzes water oxidation at the oxygen-evolving complex (OEC), a heterocubanoid calcium-tetramanganese cluster. Here, we analyze the omit electron density peaks of the OEC's metal ions in five X-ray free-electron laser PSII structures at resolutions between 2.15 and 1.95 Å. The omit peaks can be described by the total number of electrons and approximated by the variance of electron density distribution when the distributions are spherically symmetric. We show that the number of electrons of metal centers is different in the two OECs of PSII dimers, implying that the oxidation states and/or occupancies of individual metal ions are different in the two monomers. In either case, we find that the two OECs of dark-adapted PSII dimers in crystals are not fully synchronized in the S1 state. Differences in redox states of the OEC in PSII only partially account for the observation that the electron densities integrate to a smaller number of electrons than expected. Differences between the determined and expected relative electron numbers are much larger than the estimated errors, indicating heterogeneity in the OEC composition.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, United States
| | - Christopher J Gisriel
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Krystle Reiss
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Hao-Li Huang
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - William H Armstrong
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Gary W Brudvig
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, United States.,Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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3
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Moore PB. The PDB and the ribosome. J Biol Chem 2021; 296:100561. [PMID: 33744288 PMCID: PMC8038944 DOI: 10.1016/j.jbc.2021.100561] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/11/2020] [Accepted: 03/16/2021] [Indexed: 01/31/2023] Open
Abstract
This essay, which was written to commemorate the 50th anniversary of the Protein Data Bank, opens with some comments about the intentions of the scientists who pressed for its establishment and the nature of services it provides. It includes a brief account of the events that resulted in the determination of the crystal structure of the large ribosomal subunit from Haloarcula marismortui. The magnitude of the challenge the first ribosome crystal structures posed for the PDB is commented upon, and in the description of subsequent developments in the ribosome structure field that follows, it is pointed out that cryo-EM has replaced X-ray crystallography as the method of choice for investigating ribosome structure.
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Affiliation(s)
- Peter B Moore
- Department of Chemistry, Yale University, New Haven, Connecticut, USA.
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Shabalin IG, Porebski PJ, Minor W. Refining the macromolecular model - achieving the best agreement with the data from X-ray diffraction experiment. CRYSTALLOGR REV 2018; 24:236-262. [PMID: 30416256 DOI: 10.1080/0889311x.2018.1521805] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Refinement of macromolecular X-ray crystal structures involves using complex software with hundreds of different settings. The complexity of underlying concepts and the sheer amount sof instructions may make it difficult for less experienced crystallographers to achieve optimal results in their refinements. This tutorial review offers guidelines for choosing the best settings for the reciprocal-space refinement of macromolecular models and provides practical tips for manual model correction. To help aspiring crystallographers navigate the process, some of the most practically important concepts of protein structure refinement are described. Among the topics covered are the use and purpose of R-free, geometrical restraints, restraints on atomic displacement parameters (ADPs), refinement weights, various parametrizations of ADPs (full anisotropic refinement and TLS), and omit maps. We also give practical tips for manual model correction in Coot, modelling of side-chains with poor or missing density, and ligand identification, fitting, and refinement.
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Affiliation(s)
- Ivan G Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, United States.,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, 22908, United States
| | - Przemyslaw J Porebski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, United States.,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, 22908, United States
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, United States.,Center for Structural Genomics of Infectious Diseases (CSGID), Charlottesville, VA, 22908, United States
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5
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Towards Generalized Noise-Level Dependent Crystallographic Symmetry Classifications of More or Less Periodic Crystal Patterns. Symmetry (Basel) 2018. [DOI: 10.3390/sym10050133] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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6
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Wang J. Systematic analysis of residual density suggests that a major limitation in well-refined X-ray structures of proteins is the omission of ordered solvent. Protein Sci 2017; 26:1012-1023. [PMID: 28244185 DOI: 10.1002/pro.3145] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 02/21/2017] [Accepted: 02/23/2017] [Indexed: 12/23/2022]
Abstract
In the residual electron density map of a fully refined X-ray protein model, there should be no peaks arising from modeling errors or missing atoms. Any residual peaks that do occur should be contributed by random residual intensity differences between the model and the data. If the model is incomplete (i.e., some atoms are missing), there will be more positive peaks than negative ones. On the other hand, if the model includes inappropriately located atoms, there will be an excess of negative peaks. In this study, random residual peaks are quantified using the probability density function P(x), which is defined as the probability for a peak having peak height between x and x + dx. It is found that P(x) is single-exponential and symmetric for both positive and negative peaks. Thus, P(x) can be used to discriminate residual peaks contributed by random noise in complete models from residual peaks being attributable to modeling errors in incomplete models. For a number of representative structures in the PDB it is found that P(x) has far more large (greater than 5 sigma) positive peaks than large negative peaks. This excess of large positive peaks suggests that the main defect in these refined structures is the omission of ordered water molecules.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, 06520
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Wang J. X-ray radiation-induced addition of oxygen atoms to protein residues. Protein Sci 2016; 25:1407-19. [PMID: 27074249 PMCID: PMC4989999 DOI: 10.1002/pro.2934] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 04/07/2016] [Accepted: 04/11/2016] [Indexed: 02/03/2023]
Abstract
The additions of oxygen and peroxide to residues that result when proteins are exposed to the free radicals produced using the Fenton reaction or X-rays have been studied for over a century. Nevertheless little is known about the impact these modifications have on protein crystal structures. Here evidence is presented that both kinds of modifications occur in protein crystals on a significant scale during the collection of X-ray diffraction data. For example, at least 538 of the 5,351 residues of protein molecules in the crystal used to obtain the structure for photosystem II described by the PDB accession number 3ARC became oxygenated during data collection.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, 06520
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Matthews BW. Which of the 100,000 structures in the protein data bank are reliable? Protein Sci 2015; 24:589-91. [DOI: 10.1002/pro.2662] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 02/06/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Brian W. Matthews
- Institute of Molecular Biology and Department of Physics; University of Oregon; Eugene Oregon 97403
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Wang J. Estimation of the quality of refined protein crystal structures. Protein Sci 2015; 24:661-9. [PMID: 25581292 DOI: 10.1002/pro.2639] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/30/2014] [Accepted: 01/05/2015] [Indexed: 01/13/2023]
Abstract
Crystallographic R work and R free values, which are measures of the ability of the models of macromolecular structures to explain the crystallographic data on which they are based, are often used to assess structure quality. It is widely known, and confirmed here that both are sensitive to the methods used to compute them, and can be manipulated to improve the apparent quality of the model. As an alternative it is proposed here that the quality of crystallographic models should be assessed using a global goodness-of-fit metric RO2A /R work where RO2A is the number of reflections used for refinement divided by the number of nonhydrogen atoms in the structure, and R work is the working R-factor of the refined structure. Also, analysis of structures in the Protein Data Bank suggests that many data sets have been truncated at high resolution, thereby improving the R-factor statistics. To discourage this practice, it is proposed that the resolution of a dataset be defined as the resolution of the shell of data where <I/σI > falls to 1. The proposed goodness-of-fit metric encourages investigators to use all the data available rather than a truncated subset.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, 06520
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