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Ding W, Zhang T, He Y, Wang J, Wu L, Han P, Zheng C, Gu Y, Zeng L, Hao Q, Fan H. IPCAS: a direct-method-based pipeline from phasing to model building and refinement for macromolecular structure determination. J Appl Crystallogr 2020. [DOI: 10.1107/s1600576719015115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
A new version (2.0) of the pipeline IPCAS (Iterative Protein Crystal structure Automatic Solution) has been released, in which the program OASIS performs direct-method single-wavelength anomalous diffraction/single isomorphous replacement phasing and direct-method-aided partial-structure extension. IPCAS incorporates the widely used packages CCP4 and PHENIX for locating heavy atoms, density modification, molecular replacement, model building and refinement. Important extensions to the previous version of IPCAS include a resolution screening method for non-crystallographic symmetry searching, an alternate model-building protocol for avoiding premature convergence and direct-method image processing for electron microscopy maps, including single-particle cryo-EM maps. Moreover, a new graphical user interface is provided for controlling and real-time monitoring of the whole dual-space iterative process, which works as a plugin to CCP4i. Applications of the new IPCAS to difficult cases have yielded promising results, including `direct-method phasing and fragment extension' from weak anomalous diffraction signal data and `direct-method-aided partial-structure extension' from low-homology models.
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Zhang W, Zhang H, Zhang T, Fan H, Hao Q. Protein-complex structure completion using IPCAS (Iterative Protein Crystal structure Automatic Solution). ACTA ACUST UNITED AC 2015; 71:1487-92. [PMID: 26143920 DOI: 10.1107/s1399004715008597] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 05/02/2015] [Indexed: 11/10/2022]
Abstract
Protein complexes are essential components in many cellular processes. In this study, a procedure to determine the protein-complex structure from a partial molecular-replacement (MR) solution is demonstrated using a direct-method-aided dual-space iterative phasing and model-building program suite, IPCAS (Iterative Protein Crystal structure Automatic Solution). The IPCAS iteration procedure involves (i) real-space model building and refinement, (ii) direct-method-aided reciprocal-space phase refinement and (iii) phase improvement through density modification. The procedure has been tested with four protein complexes, including two previously unknown structures. It was possible to use IPCAS to build the whole complex structure from one or less than one subunit once the molecular-replacement method was able to give a partial solution. In the most challenging case, IPCAS was able to extend to the full length starting from less than 30% of the complex structure, while conventional model-building procedures were unsuccessful.
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Affiliation(s)
- Weizhe Zhang
- Department of Physiology, University of Hong Kong, Hong Kong
| | - Hongmin Zhang
- Department of Physiology, University of Hong Kong, Hong Kong
| | - Tao Zhang
- Institute of Physics, Chinese Academy of Sciences, Beijing 100080, People's Republic of China
| | - Haifu Fan
- Institute of Physics, Chinese Academy of Sciences, Beijing 100080, People's Republic of China
| | - Quan Hao
- Department of Physiology, University of Hong Kong, Hong Kong
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Bunkóczi G, McCoy AJ, Echols N, Grosse-Kunstleve RW, Adams PD, Holton JM, Read RJ, Terwilliger TC. Macromolecular X-ray structure determination using weak, single-wavelength anomalous data. Nat Methods 2015; 12:127-30. [PMID: 25532136 PMCID: PMC4312553 DOI: 10.1038/nmeth.3212] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 11/11/2014] [Indexed: 01/09/2023]
Abstract
We describe a likelihood-based method for determining the substructure of anomalously scattering atoms in macromolecular crystals that allows successful structure determination by single-wavelength anomalous diffraction (SAD) X-ray analysis with weak anomalous signal. With the use of partial models and electron density maps in searches for anomalously scattering atoms, testing of alternative values of parameters and parallelized automated model-building, this method has the potential to extend the applicability of the SAD method in challenging cases.
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Affiliation(s)
- Gábor Bunkóczi
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England
| | - Airlie J. McCoy
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England
| | - Nathaniel Echols
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - Ralf W. Grosse-Kunstleve
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - Paul D. Adams
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - James M. Holton
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158
| | - Randy J. Read
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England
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Fan H, Gu Y, He Y, Lin Z, Wang J, Yao D, Zhang T. Applications of direct methods in protein crystallography for dealing with diffraction data down to 5 Å resolution. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2014; 70:239-47. [PMID: 24815973 DOI: 10.1107/s2053273313034864] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 12/30/2013] [Indexed: 11/10/2022]
Abstract
Apart from solving the heavy-atom substructure in proteins and ab initio phasing of protein diffraction data at atomic resolution, direct methods have also been successfully combined with other protein crystallographic methods in dealing with diffraction data far below atomic resolution, leading to significantly improved results. In this respect, direct methods provide phase constraints in reciprocal space within a dual-space iterative framework rather than solve the phase problem independently. Applications of this type of direct methods to difficult SAD phasing, model completion and low-resolution phase extension will be described in detail.
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Affiliation(s)
- Haifu Fan
- Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, People's Republic of China
| | - Yuanxin Gu
- Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, People's Republic of China
| | - Yao He
- Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, People's Republic of China
| | - Zhengjiong Lin
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Jiawei Wang
- School of Life Sciences, Tsinghua University, Beijing, 100084, People's Republic of China
| | - Deqiang Yao
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, People's Republic of China
| | - Tao Zhang
- Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, People's Republic of China
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5
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Fukakusa S, Kawahara K, Nakamura S, Iwashita T, Baba S, Nishimura M, Kobayashi Y, Honda T, Iida T, Taniguchi T, Ohkubo T. Structure of the CFA/III major pilin subunit CofA from human enterotoxigenic Escherichia coli determined at 0.90 Å resolution by sulfur-SAD phasing. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1418-29. [PMID: 22993096 DOI: 10.1107/s0907444912034464] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 08/02/2012] [Indexed: 11/11/2022]
Abstract
CofA, a major pilin subunit of colonization factor antigen III (CFA/III), forms pili that mediate small-intestinal colonization by enterotoxigenic Escherichia coli (ETEC). In this study, the crystal structure of an N-terminally truncated version of CofA was determined by single-wavelength anomalous diffraction (SAD) phasing using five sulfurs in the protein. Given the counterbalance between anomalous signal strength and the undesired X-ray absorption of the solvent, diffraction data were collected at 1.5 Å resolution using synchrotron radiation. These data were sufficient to elucidate the sulfur substructure at 1.38 Å resolution. The low solvent content (29%) of the crystal necessitated that density modification be performed with an additional 0.9 Å resolution data set to reduce the phase error caused by the small sulfur anomalous signal. The CofA structure showed the αβ-fold typical of type IVb pilins and showed high structural homology to that of TcpA for toxin-coregulated pili of Vibrio cholerae, including spatial distribution of key residues critical for pilin self-assembly. A pilus-filament model of CofA was built by computational docking and molecular-dynamics simulation using the previously reported filament model of TcpA as a structural template. This model revealed that the CofA filament surface was highly negatively charged and that a 23-residue-long loop between the α1 and α2 helices filled the gap between the pilin subunits. These characteristics could provide a unique binding epitope for the CFA/III pili of ETEC compared with other type IVb pili.
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Affiliation(s)
- Shunsuke Fukakusa
- Department of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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Li Y, Gao Z, Hou H, Li L, Zhang J, Yang H, Dong Y, Tan H. Crystal structure and site-directed mutagenesis of a nitroalkane oxidase from Streptomyces ansochromogenes. Biochem Biophys Res Commun 2011; 405:344-8. [DOI: 10.1016/j.bbrc.2010.12.050] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Accepted: 12/08/2010] [Indexed: 11/30/2022]
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Zhou YF, Nan B, Nan J, Ma Q, Panjikar S, Liang YH, Wang Y, Su XD. C4-dicarboxylates sensing mechanism revealed by the crystal structures of DctB sensor domain. J Mol Biol 2008; 383:49-61. [PMID: 18725229 DOI: 10.1016/j.jmb.2008.08.010] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2008] [Revised: 08/02/2008] [Accepted: 08/06/2008] [Indexed: 11/19/2022]
Abstract
C(4)-dicarboxylates are the major carbon and energy sources during the symbiotic growth of rhizobia. Responses to C(4)-dicarboxylates depend on typical two-component systems (TCS) consisting of a transmembrane sensor histidine kinase and a cytoplasmic response regulator. The DctB-DctD system is the first identified TCS for C(4)-dicarboxylates sensing. Direct ligand binding to the sensor domain of DctB is believed to be the first step of the sensing events. In this report, the water-soluble periplasmic sensor domain of Sinorhizobium meliloti DctB (DctBp) was studied, and three crystal structures were solved: the apo protein, a complex with C(4) succinate, and a complex with C(3) malonate. Different from the two structurally known CitA family of carboxylate sensor proteins CitA and DcuS, the structure of DctBp consists of two tandem Per-Arnt-Sim (PAS) domains and one N-terminal helical region. Only the membrane-distal PAS domain was found to bind the ligands, whereas the proximal PAS domain was empty. Comparison of DctB, CitA, and DcuS suggests a detailed stereochemistry of C(4)-dicarboxylates ligand perception. The structures of the different ligand binding states of DctBp also revealed a series of conformational changes initiated upon ligand binding and propagated to the N-terminal domain responsible for dimerization, providing insights into understanding the detailed mechanism of the signal transduction of TCS histidine kinases.
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Affiliation(s)
- Yan-Feng Zhou
- National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
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Withers-Martinez C, Haire LF, Hackett F, Walker PA, Howell SA, Smerdon SJ, Dodson GG, Blackman MJ. Malarial EBA-175 region VI crystallographic structure reveals a KIX-like binding interface. J Mol Biol 2007; 375:773-81. [PMID: 18036613 DOI: 10.1016/j.jmb.2007.10.071] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2007] [Revised: 10/26/2007] [Accepted: 10/26/2007] [Indexed: 10/22/2022]
Abstract
The malaria parasite proliferates in the bloodstream of its vertebrate host by invading and replicating within erythrocytes. To achieve successful invasion, a number of discrete and essential events need to take place at the parasite-host cell interface. Erythrocyte-binding antigen 175 (EBA-175) is a member of a family of Plasmodium falciparum erythrocyte-binding proteins involved in the formation of a tight junction, a necessary step in invasion. Here we present the crystal structure of EBA-175 region VI (rVI), a cysteine-rich domain that is highly conserved within the protein family and is essential for EBA-175 trafficking. The structure was solved by selenomethionine single-wavelength anomalous dispersion at 1.8 A resolution. It reveals a homodimer, containing in each subunit a compact five-alpha-helix core that is stabilized by four conserved disulfide bridges. rVI adopts a novel fold that is likely conserved across the protein family, indicating a conserved function. It shows no similarity to the Duffy-binding-like domains of EBA-175 involved in erythrocyte binding, indicating a distinct role. Remarkably, rVI possesses structural features related to the KIX-binding domain of the coactivator CREB-binding protein, supporting the binding and trafficking roles that have been ascribed to it and providing a rational basis for further experimental investigation of its function.
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Wu Y, Sha B. Crystal structure of yeast mitochondrial outer membrane translocon member Tom70p. Nat Struct Mol Biol 2006; 13:589-93. [PMID: 16767096 DOI: 10.1038/nsmb1106] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Accepted: 05/10/2006] [Indexed: 11/09/2022]
Abstract
A majority of the proteins targeted to the mitochondria are transported through the translocase of the outer membrane (TOM) complex. Tom70 is a major surface receptor for mitochondrial protein precursors in the TOM complex. To investigate how Tom70 receives the mitochondrial protein precursors, we have determined the crystal structure of yeast Tom70p to 3.0 A. Tom70p forms a homodimer in the crystal. Each subunit consists primarily of tetratricopeptide repeat (TPR) motifs, which are organized into a right-handed superhelix. The TPR motifs in the N-terminal domain of Tom70p form a peptide-binding groove for the C-terminal EEVD motif of Hsp70, whereas the C-terminal domain of Tom70p contains a large pocket that may be the binding site for mitochondrial precursors. The crystal structure of Tom70p provides insights into the mechanisms of precursor transport across the mitochondrion's outer membrane.
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Affiliation(s)
- Yunkun Wu
- Department of Cell Biology, Center for Biophysical Sciences and Engineering, MCLM 364, 1918 Univ. Blvd., University of Alabama at Birmingham, Birmingham, Alabama 35294-0005, USA
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