EMDataBank.org: Unified Data Resource for CryoEM

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2010 Oct 12

PMID 20935055

Citations 142

Authors

Catherine L Lawson

Matthew L Baker

Christoph Best

Chunxiao Bi

Matthew Dougherty

Powei Feng

Glen van Ginkel

Batsal Devkota

Ingvar Lagerstedt

Steven J Ludtke

Richard H Newman

Tom J Oldfield

Ian Rees

Gaurav Sahni

Raul Sala

Sameer Velankar

Joe Warren

John D Westbrook

Kim Henrick

Gerard J Kleywegt

Helen M Berman

Wah Chiu

Affiliations

Soon will be listed here.

Abstract

Cryo-electron microscopy reconstruction methods are uniquely able to reveal structures of many important macromolecules and macromolecular complexes. EMDataBank.org, a joint effort of the Protein Data Bank in Europe (PDBe), the Research Collaboratory for Structural Bioinformatics (RCSB) and the National Center for Macromolecular Imaging (NCMI), is a global 'one-stop shop' resource for deposition and retrieval of cryoEM maps, models and associated metadata. The resource unifies public access to the two major archives containing EM-based structural data: EM Data Bank (EMDB) and Protein Data Bank (PDB), and facilitates use of EM structural data of macromolecules and macromolecular complexes by the wider scientific community.

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References

Baker M, Baker M, Hryc C, DiMaio F . Analyses of subnanometer resolution cryo-EM density maps. Methods Enzymol. 2010; 483:1-29. PMC: 3107677. DOI: 10.1016/S0076-6879(10)83001-0. View

Williams K . Three-dimensional structure of the ion-coupled transport protein NhaA. Nature. 2000; 403(6765):112-5. DOI: 10.1038/47534. View

Tang J, Pan J, Havens W, Ochoa W, Guu T, Ghabrial S . Backbone trace of partitivirus capsid protein from electron cryomicroscopy and homology modeling. Biophys J. 2010; 99(2):685-94. PMC: 2905076. DOI: 10.1016/j.bpj.2010.04.058. View

Clare D, Orlova E . 4.6A Cryo-EM reconstruction of tobacco mosaic virus from images recorded at 300 keV on a 4k x 4k CCD camera. J Struct Biol. 2010; 171(3):303-8. PMC: 2939825. DOI: 10.1016/j.jsb.2010.06.011. View

Yu X, Egelman E . The RecA hexamer is a structural homologue of ring helicases. Nat Struct Biol. 1997; 4(2):101-4. DOI: 10.1038/nsb0297-101. View

Fernandez J, Luque D, Caston J, Carrascosa J . Sharpening high resolution information in single particle electron cryomicroscopy. J Struct Biol. 2008; 164(1):170-5. DOI: 10.1016/j.jsb.2008.05.010. View

Jiang W, Baker M, Wu Q, Bajaj C, Chiu W . Applications of a bilateral denoising filter in biological electron microscopy. J Struct Biol. 2003; 144(1-2):114-22. DOI: 10.1016/j.jsb.2003.09.028. View

Mukhopadhyay S, Kim B, Chipman P, Rossmann M, Kuhn R . Structure of West Nile virus. Science. 2003; 302(5643):248. DOI: 10.1126/science.1089316. View

Tan R, Devkota B, Harvey S . YUP.SCX: coaxing atomic models into medium resolution electron density maps. J Struct Biol. 2008; 163(2):163-74. PMC: 2702770. DOI: 10.1016/j.jsb.2008.05.001. View

10.

Ledizet M, Kar K, Foellmer H, Wang T, Bushmich S, Anderson J . A recombinant envelope protein vaccine against West Nile virus. Vaccine. 2005; 23(30):3915-24. DOI: 10.1016/j.vaccine.2005.03.006. View

11.

Berman H, Henrick K, Nakamura H . Announcing the worldwide Protein Data Bank. Nat Struct Biol. 2003; 10(12):980. DOI: 10.1038/nsb1203-980. View

12.

Kuhn R, Zhang W, Rossmann M, Pletnev S, Corver J, Lenches E . Structure of dengue virus: implications for flavivirus organization, maturation, and fusion. Cell. 2002; 108(5):717-25. PMC: 4152842. DOI: 10.1016/s0092-8674(02)00660-8. View

13.

Xiong Y . From electron microscopy to X-ray crystallography: molecular-replacement case studies. Acta Crystallogr D Biol Crystallogr. 2007; 64(Pt 1):76-82. PMC: 2394795. DOI: 10.1107/S090744490705398X. View

14.

Hartshorn M . AstexViewer: a visualisation aid for structure-based drug design. J Comput Aided Mol Des. 2003; 16(12):871-81. DOI: 10.1023/a:1023813504011. View

15.

Baker M, Ju T, Chiu W . Identification of secondary structure elements in intermediate-resolution density maps. Structure. 2007; 15(1):7-19. PMC: 1810566. DOI: 10.1016/j.str.2006.11.008. View

16.

Trabuco L, Villa E, Schreiner E, Harrison C, Schulten K . Molecular dynamics flexible fitting: a practical guide to combine cryo-electron microscopy and X-ray crystallography. Methods. 2009; 49(2):174-80. PMC: 2753685. DOI: 10.1016/j.ymeth.2009.04.005. View

17.

Baker M, Jiang W, Rixon F, Chiu W . Common ancestry of herpesviruses and tailed DNA bacteriophages. J Virol. 2005; 79(23):14967-70. PMC: 1287596. DOI: 10.1128/JVI.79.23.14967-14970.2005. View

18.

Xing L, Li T, Mayazaki N, Simon M, Wall J, Moore M . Structure of hepatitis E virion-sized particle reveals an RNA-dependent viral assembly pathway. J Biol Chem. 2010; 285(43):33175-33183. PMC: 2963395. DOI: 10.1074/jbc.M110.106336. View

19.

Sindelar C, Downing K . The beginning of kinesin's force-generating cycle visualized at 9-A resolution. J Cell Biol. 2007; 177(3):377-85. PMC: 2064809. DOI: 10.1083/jcb.200612090. View

20.

DiMaio F, Tyka M, Baker M, Chiu W, Baker D . Refinement of protein structures into low-resolution density maps using rosetta. J Mol Biol. 2009; 392(1):181-90. PMC: 3899897. DOI: 10.1016/j.jmb.2009.07.008. View