EMDataBank.org: unified data resource for CryoEM

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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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Most cited references 65

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Structure of the dengue virus envelope protein after membrane fusion.

Yorgo Modis, Steven Ogata, David K. Clements … (2004)

Dengue virus enters a host cell when the viral envelope glycoprotein, E, binds to a receptor and responds by conformational rearrangement to the reduced pH of an endosome. The conformational change induces fusion of viral and host-cell membranes. A three-dimensional structure of the soluble E ectodomain (sE) in its trimeric, postfusion state reveals striking differences from the dimeric, prefusion form. The elongated trimer bears three 'fusion loops' at one end, to insert into the host-cell membrane. Their structure allows us to model directly how these fusion loops interact with a lipid bilayer. The protein folds back on itself, directing its carboxy terminus towards the fusion loops. We propose a fusion mechanism driven by essentially irreversible conformational changes in E and facilitated by fusion-loop insertion into the outer bilayer leaflet. Specific features of the folded-back structure suggest strategies for inhibiting flavivirus entry.

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The PyMol molecular graphics system

WL DeLano, W. L. Delano, WL. Delano … (2002)

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Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy.

R. Henderson, J.M. Baldwin, T.A. Ceska … (1990)

The light-driven proton pump bacteriorhodopsin occurs naturally as two-dimensional crystals. A three-dimensional density map of the structure, at near-atomic resolution, has been obtained by studying the crystals using electron cryo-microscopy to obtain electron diffraction patterns and high-resolution micrographs. New methods were developed for analysing micrographs from tilted specimens, incorporating methods previously developed for untilted specimens that enable large areas to be analysed and corrected for distortions. Data from 72 images, from both tilted and untilted specimens, were analysed to produce the phases of 2700 independent Fourier components of the structure. The amplitudes of these components were accurately measured from 150 diffraction patterns. Together, these data represent about half of the full three-dimensional transform to 3.5 A. The map of the structure has a resolution of 3.5 A in a direction parallel to the membrane plane but lower than this in the perpendicular direction. It shows many features in the density that are resolved from the main density of the seven alpha-helices. We interpret these features as the bulky aromatic side-chains of phenylalanine, tyrosine and tryptophan residues. There is also a very dense feature, which is the beta-ionone ring of the retinal chromophore. Using these bulky side-chains as guide points and taking account of bulges in the helices that indicate smaller side-chains such as leucine, a complete atomic model for bacteriorhodopsin between amino acid residues 8 and 225 has been built. There are 21 amino acid residues, contributed by all seven helices, surrounding the retinal and 26 residues, contributed by five helices, forming the proton pathway or channel. Ten of the amino acid residues in the middle of the proton channel are also part of the retinal binding site. The model also provides a useful basis for consideration of the mechanism of proton pumping and allows a consistent interpretation of a great deal of other experimental data. In particular, the structure suggests that pK changes in the Schiff base must act as the means by which light energy is converted into proton pumping pressure in the channel. Asp96 is on the pathway from the cytoplasm to the Schiff base and Asp85 is on the pathway from the Schiff base to the extracellular surface.

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Author and article information

Journal

Journal ID (nlm-ta): Nucleic Acids Res

Journal ID (publisher-id): nar

Journal ID (hwp): nar

Title: Nucleic Acids Research

Publisher: Oxford University Press

ISSN (Print): 0305-1048

ISSN (Electronic): 1362-4962

Publication date Collection: January 2011

Publication date (Print): January 2011

Publication date (Electronic): 8 October 2010

Publication date PMC-release: 8 October 2010

Volume: 39

Issue: Database issue , Database issue

Pages: D456-D464

Affiliations

¹Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 610 Taylor Road Piscataway, NJ 08854, ²Department of Biochemistry and Molecular Biology, National Center for Macromolecular Imaging, Verna and Marrs McLean, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 70030, USA, ³Protein Data Bank in Europe, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and ⁴Department of Computer Science, Rice University, 6100 South Main, Houston, TX 77251, USA

Author notes

*To whom correspondence should be addressed. Tel: +1 732 445 5494; Fax: +1 732 445 4320; Email: cathy.lawson@ 123456rutgers.edu

Correspondence may also be addressed to Wah Chiu. Tel: +1 713 798 6989; Fax: +1 713 798 8682; Email: wah@ 123456bcm.edu

Present addresses: Christoph Best, Google UK Ltd, Belgrave House, 76 Buckingham Palace Road, London SW1W 9TQ, UK.

Chunxiao Bi, San Diego Supercomputer Center (SDSC) and Skaggs School of Pharmacy and Pharmaceutical Sciences University of California, San Diego (UCSD), 9500 Gilman Drive, La Jolla, CA 92093-0537, USA.

Richard H. Newman, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK.

Article

Publisher ID: gkq880

DOI: 10.1093/nar/gkq880

PMC ID: 3013769

PubMed ID: 20935055

SO-VID: 06f93f3b-f1ea-46b7-8584-4295f667b6aa

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This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

EMDataBank.org: unified data resource for CryoEM

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Decoding Infection and Transmission

Most cited references 65

Structure of the dengue virus envelope protein after membrane fusion.

The PyMol molecular graphics system

Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy.

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