Cryo-EM of macromolecular assemblies at near-atomic resolution

被引:64
作者
Baker, Matthew L. [1 ]
Zhang, Junjie [1 ]
Ludtke, Steven J. [1 ]
Chiu, Wah [1 ]
机构
[1] Baylor Coll Med, Natl Ctr Macromol Imaging, Verna & Marrs Mclean Dept Biochem & Mol Biol, Houston, TX 77030 USA
基金
美国国家科学基金会; 美国国家卫生研究院;
关键词
SECONDARY STRUCTURE ELEMENTS; PROTEIN-STRUCTURE; ELECTRON CRYOMICROSCOPY; SINGLE PARTICLES; PREDICTION; RECONSTRUCTION; MECHANISM; CHAPERONIN; CLOSURE; IMAGES;
D O I
10.1038/nprot.2010.126
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
With single-particle electron cryomicroscopy (cryo-EM), it is possible to visualize large, macromolecular assemblies in near-native states. Although subnanometer resolutions have been routinely achieved for many specimens, state of the art cryo-EM has pushed to near-atomic (3.3-4.6 angstrom) resolutions. At these resolutions, it is now possible to construct reliable atomic models directly from the cryo-EM density map. In this study, we describe our recently developed protocols for performing the three-dimensional reconstruction and modeling of Mm-cpn, a group II chaperonin, determined to 4.3 angstrom resolution. This protocol, utilizing the software tools EMAN, Gorgon and Coot, can be adapted for use with nearly all specimens imaged with cryo-EM that target beyond 5 angstrom resolution. Additionally, the feature recognition and computational modeling tools can be applied to any near-atomic resolution density maps, including those from X-ray crystallography.
引用
收藏
页码:1697 / 1708
页数:12
相关论文
共 41 条
[11]   Coot:: model-building tools for molecular graphics [J].
Emsley, P ;
Cowtan, K .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2004, 60 :2126-2132
[12]   FREALIGN: High-resolution refinement of single particle structures [J].
Grigorieff, Nikolaus .
JOURNAL OF STRUCTURAL BIOLOGY, 2007, 157 (01) :117-125
[13]   Bridging the information gap: Computational tools for intermediate resolution structure interpretation [J].
Jiang, W ;
Baker, ML ;
Ludtke, SJ ;
Chiu, W .
JOURNAL OF MOLECULAR BIOLOGY, 2001, 308 (05) :1033-1044
[14]   Backbone structure of the infectious ε15 virus capsid revealed by electron cryomicroscopy [J].
Jiang, Wen ;
Baker, Matthew L. ;
Jakana, Joanita ;
Weigele, Peter R. ;
King, Jonathan ;
Chiu, Wah .
NATURE, 2008, 451 (7182) :1130-U12
[15]   Prediction of β-turns and β-turn types by a novel bidirectional Elman-type recurrent neural network with multiple output layers (MOLEBRNN) [J].
Kirschner, Andreas ;
Frishman, Dmitrij .
GENE, 2008, 422 (1-2) :22-29
[16]   Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-path Simulated Annealing optimization algorithm [J].
Liu, Xiangan ;
Jiang, Wen ;
Jakana, Joanita ;
Chiu, Wah .
JOURNAL OF STRUCTURAL BIOLOGY, 2007, 160 (01) :11-27
[17]   Structural changes in a marine podovirus associated with release of its genome into Prochlorococcus [J].
Liu, Xiangan ;
Zhang, Qinfen ;
Murata, Kazuyoshi ;
Baker, Matthew L. ;
Sullivan, Matthew B. ;
Fu, Caroline ;
Dougherty, Matthew T. ;
Schmid, Michael F. ;
Osburne, Marcia S. ;
Chisholm, Sallie W. ;
Chiu, Wah .
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 2010, 17 (07) :830-U76
[18]   The pore structure of the closed RyR1 channel [J].
Ludtke, SJ ;
Serysheva, II ;
Hamilton, SL ;
Chiu, W .
STRUCTURE, 2005, 13 (08) :1203-1211
[19]   EMAN: Semiautomated software for high-resolution single-particle reconstructions [J].
Ludtke, SJ ;
Baldwin, PR ;
Chiu, W .
JOURNAL OF STRUCTURAL BIOLOGY, 1999, 128 (01) :82-97
[20]   A 11.5 Å single particle reconstruction of GroEL using EMAN [J].
Ludtke, SJ ;
Jakana, J ;
Song, JL ;
Chuang, DT ;
Chiu, W .
JOURNAL OF MOLECULAR BIOLOGY, 2001, 314 (02) :253-262