title: Protein-complex structure completion using IPCAS (Iterative Protein Crystal structure Automatic Solution).
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.
authors.affiliation: Department of Physiology, University of Hong Kong, Hong Kong.
authors.forename: Weizhe
authors.initials: W
authors.lastname: Zhang
authors.affiliation: Department of Physiology, University of Hong Kong, Hong Kong.
authors.forename: Hongmin
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Institute of Physics, Chinese Academy of Sciences, Beijing 100080, People's Republic of China.
authors.forename: Tao
authors.initials: T
authors.lastname: Zhang
authors.affiliation: Institute of Physics, Chinese Academy of Sciences, Beijing 100080, People's Republic of China.
authors.forename: Haifu
authors.initials: H
authors.lastname: Fan
authors.affiliation: Department of Physiology, University of Hong Kong, Hong Kong.
authors.forename: Quan
authors.initials: Q
authors.lastname: Hao
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry; D018360:Crystallography, X-Ray; D004268:DNA-Binding Proteins / Q000737:chemistry; D004926:Escherichia coli / Q000737:chemistry; D029968:Escherichia coli Proteins / Q000737:chemistry; D056506:Geobacillus / Q000737:chemistry; D006801:Humans; D007711:Klebsiella pneumoniae / Q000737:chemistry; D058619:Maltose-Binding Proteins / Q000737:chemistry; D008958:Models, Molecular; D028861:Nuclear Pore Complex Proteins / Q000737:chemistry; D011487:Protein Conformation; D055503:Protein Multimerization; D011506:Proteins / Q000737:chemistry*; D014734:Vibrio cholerae / Q000737:chemistry; D001618:beta-Lactamases / Q000737:chemistry
chemical_list: D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; C031908:H-NS protein, bacteria; D058619:Maltose-Binding Proteins; D028861:Nuclear Pore Complex Proteins; D011506:Proteins; D001618:beta-Lactamases; C552864:beta-lactamase NDM-1
keywords: IPCAS; iterative phasing; model building; protein complexes