Building the atomic model of a boreal lake virus of unknown fold in a 3.9 Å cryo-EM map

被引：2

作者：

De Colibus, Luigi ^{[1
]}

Stuart, David I. ^{[1
,2
]}

机构：

[1] Univ Oxford, Div Struct Biol, Henry Wellcome Bldg Genom Med, Oxford OX3 7BN, England

[2] Diamond Light Source Ltd, Harwell Sci & Innovat Campus, Didcot OX11 0DE, Oxon, England

来源：

JOURNAL OF STRUCTURAL BIOLOGY | 2018年 / 202卷 / 01期

基金：

英国医学研究理事会;

关键词：

Cryo electron microscopy; Model building; Density modification; Virus structure; AUTOMATED PROTEIN-STRUCTURE; I-TASSER; VISUALIZATION; VALIDATION; REFINEMENT; PREDICTION; RESOLUTION; INSIGHTS; REVEALS; SYSTEM;

D O I：

10.1016/j.jsb.2017.10.010

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

We report here the protocol adopted to build the atomic model of the newly discovered virus FLiP (Elavobacterium infecting, lipid-containing phage) into 3.9 angstrom cryo-electron microscopy (cryo-EM) maps. In particular, this report discusses the combination of density modification procedures, automatic model building and bioinformatics tools applied to guide the tracing of the major capsid protein (MCP) of this virus. The protocol outlined here may serve as a reference for future structural determination by cryo-EM of viruses lacking detectable structural homologues.

引用

页码：94 / 99

页数：6

共 35 条

[1] Insights into assembly from structural analysis of bacteriophage PRD1 [J].

Abrescia, NGA ;

Cockburn, JJB ;

Grimes, JM ;

Sutton, GC ;

Diprose, JM ;

Butcher, SJ ;

Fuller, SD ;

Martín, CS ;

Burnett, RM ;

Stuart, DI ;

Bamford, DH ;

Bamford, JKH .

NATURE, 2004, 432 (7013) :68-74

[2] Insights into virus evolution and membrane biogenesis from the structure of the marine lipid-containing bacteriophage PM2 [J].

Abrescia, Nicola G. A. ;

Grimes, Jonathan M. ;

Kivela, Hanna M. ;

Assenberg, Rene ;

Sutton, Geoff C. ;

Butcher, Sarah J. ;

Bamford, Jaana K. H. ;

Bamford, Dennis H. ;

Stuart, David I. .

MOLECULAR CELL, 2008, 31 (05) :749-761

[3] PHENIX: a comprehensive Python']Python-based system for macromolecular structure solution [J].

Adams, Paul D. ;

Afonine, Pavel V. ;

Bunkoczi, Gabor ;

Chen, Vincent B. ;

Davis, Ian W. ;

Echols, Nathaniel ;

Headd, Jeffrey J. ;

Hung, Li-Wei ;

Kapral, Gary J. ;

Grosse-Kunstleve, Ralf W. ;

McCoy, Airlie J. ;

Moriarty, Nigel W. ;

Oeffner, Robert ;

Read, Randy J. ;

Richardson, David C. ;

Richardson, Jane S. ;

Terwilliger, Thomas C. ;

Zwart, Peter H. .

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2010, 66 :213-221

[4]

AFONINE PV, 2013, COMPUT CRYSTALLOGR N, V0004

[5] Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles [J].

Bai, Xiao-chen ;

Fernandez, Israel S. ;

McMullan, Greg ;

Scheres, Sjors H. W. .

ELIFE, 2013, 2

[6]

Barad BA, 2015, NAT METHODS, V12, P943, DOI [10.1038/NMETH.3541, 10.1038/nmeth.3541]

[7] Beam-induced motion of vitrified specimen on holey carbon film [J].

Brilot, Axel F. ;

Chen, James Z. ;

Cheng, Anchi ;

Pan, Junhua ;

Harrison, Stephen C. ;

Potter, Clinton S. ;

Carragher, Bridget ;

Henderson, Richard ;

Grigorieff, Nikolaus .

JOURNAL OF STRUCTURAL BIOLOGY, 2012, 177 (03) :630-637

[8] Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions [J].

Brown, Alan ;

Long, Fei ;

Nicholls, Robert A. ;

Toots, Jaan ;

Emsley, Paul ;

Murshudov, Garib .

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2015, 71 :136-153

[9] 2.8 Å resolution reconstruction of the Thermoplasma acidophilum 20S proteasome using cryo-electron microscopy [J].

Campbell, Melody G. ;

Veesler, David ;

Cheng, Anchi ;

Potter, Clinton S. ;

Carragher, Bridget .

ELIFE, 2015, 4 :1-22

[10] Movies of Ice-Embedded Particles Enhance Resolution in Electron Cryo-Microscopy [J].

Campbell, Melody G. ;

Cheng, Anchi ;

Brilot, Axel F. ;

Moeller, Arne ;

Lyumkis, Dmitry ;

Veesler, David ;

Pan, Junhua ;

Harrison, Stephen C. ;

Potter, Clinton S. ;

Carragher, Bridget ;

Grigorieff, Nikolaus .

STRUCTURE, 2012, 20 (11) :1823-1828

← 1 2 3 4 →