Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB

Journal of Structural Biology

Volumn 184, Issue 2, 2013, Pages 173-181

  Lagerstedt, Ingvar ^a   Moore, William J ^b   Patwardhan, Ardan ^a   Sanz García, Eduardo ^a   Best, Christoph ^a,c   Swedlow, Jason R ^b   Kleywegt, Gerard J ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b UNIVERSITY OF DUNDEE   (United Kingdom)

^c GOOGLE   (United Kingdom)

Author keywords

Electron microscopy; Electron tomography; Macromolecular structure; Visualisation

Indexed keywords

ARTICLE; AUDIOVISUAL EQUIPMENT; DATA ANALYSIS; ELECTRON MICROSCOPY; ELECTRON TOMOGRAPHY; IMAGE RECONSTRUCTION; INSTRUMENT VALIDATION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATA BANK; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; THREE DIMENSIONAL IMAGING; WEB BROWSER;

3DEM; ELECTRON MICROSCOPY; ELECTRON MICROSCOPY DATA BANK; ELECTRON MICROSCOPY VALIDATION TASK FORCE; ELECTRON TOMOGRAPHY; EM VTC; EMDB; FOURIER SHELL CORRELATION; FSC; MACROMOLECULAR STRUCTURE; OAV; OME; OME REMOTE OBJECTS; OMERO; OPEN ASTEX VIEWER; OPEN MICROSCOPY ENVIRONMENT; PDB; PDBE; PROTEIN DATA BANK; PROTEIN DATA BANK IN EUROPE; THREE-DIMENSIONAL ELECTRON MICROSCOPY; VISUALISATION; WORLDWIDE PROTEIN DATA BANK; WWPDB;

DATABASES, PROTEIN; ELECTRON MICROSCOPE TOMOGRAPHY; IMAGING, THREE-DIMENSIONAL; INTERNET; MODELS, MOLECULAR; PROTEIN STRUCTURE, QUATERNARY; PROTEINS; SOFTWARE;

EID: 84887221465     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2013.09.021     Document Type: Article

References (44)

1. Abe K., Tani K., Fujiyoshi Y. Conformational rearrangement of gastric H(+), K(+)-ATPase induced by an acid suppressant. Nat. Commun. 2011, 2:155.
2. +-ATPase with a single occupied cation-binding site. Proc. Natl. Acad. Sci. USA 2012, 109:18401-18406.
3. Allan C., Burel J.-M., Moore J., Blackburn C., Linkert M., Loynton S., MacDonald D., Moore W.J., Neves C., Patterson A., Porter M., Tarkowska A., Loranger B., Avondo J., Lagerstedt I., Lianas L., Leo S., Hands K., Hay R.T., Patwardhan A., Best C., Kleywegt G.J., Zanetti G., Swedlow J.R. OMERO: flexible, model-driven data management for experimental biology. Nat. Methods 2012, 9:245-253.
4. Anger A.M., Armache J.-P., Berninghausen O., Habeck M., Subklewe M., Wilson D.N., Beckmann R. Structures of the human and Drosophila 80S ribosome. Nature 2013, 497:80-85.
5. Behrmann E., Mueller M., Penczek P.A., Mannherz H.G., Manstein D.J., Raunser S. Structure of the rigor actin-tropomyosin-myosin complex. Cell 2012, 150:327-338. (Cambridge, Mass.).
6. Berman H.M., Henrick K., Nakamura H. Announcing the worldwide Protein Data Bank. Nat. Struct. Biol. 2003, 10:980.
7. Branden C., Tooze J. Introduction to Protein Structure 1991, Garland Publishing, New York and London, pp. 276-277.
8. Connolly M.L. J. Am. Chem. Soc. 1985, 107:1118-1124.
9. DeLano W.L. The PyMOL Molecular Graphics System (2002) 2002, DeLano Scientific, San Carlos, CA, USA, http://www.pymol.org
10. Dowell R.D., Jokerst R.M., Day A., Eddy S.R., Stein L. The distributed annotation system. BMC Bioinform. 2001, 2:7.
11. Fujii T., Cheung M., Blanco A., Kato T., Blocker A.J., Namba K. Structure of a type III secretion needle at 7-A resolution provides insights into its assembly and signaling mechanisms. Proc. Natl. Acad. Sci. USA 2012, 109:4461-4466.
12. Ge P., Zhou Z.H. Hydrogen-bonding networks and RNA bases revealed by cryo electron microscopy suggest a triggering mechanism for calcium switches. Proc. Natl. Acad. Sci. USA 2011, 108:9637-9642.
13. Gerlach B., Kleinschmidt J.A., Bottcher B. Conformational changes in adeno-associated virus type 1 induced by genome packaging. J. Mol. Biol. 2011, 409:427-438.
14. Greber B.J., Boehringer D., Montellese C., Ban N. Nat. Struct. Mol. Biol. 2012, 19:1228-1233.
15. Halic M., Becker T., Pool M.R., Spahn C.M., Grassucci R.A., Frank J., Beckmann R. Structure of the signal recognition particle interacting with the elongation-arrested ribosome. Nature 2004, 427:808-814.
16. Harauz G., van Heel M. Exact filters for general geometry three dimensional reconstruction. Optik 1986, 73:146-156.
17. Hartshorn M. Astex Viewer: a visualisation aid for structure-based drug design. J. Comput. Aided Mol. Des. 2002, 16:871-881.
18. Henderson R., Sali A., Baker M.L., Carragher B., Devkota B., Downing K.H., Egelman E., Feng Z., Frank J., Grigorieff N., Jiang W., Ludtke S.J., Medalia O., Penczek P.A., Rosenthal P.B., Rossmann M.G., Schmid M.F., Schröder G.F., Steven A.C., Stokes D.L., Westbrook J.D., Wriggers W., Yang H., Young J., Berman H.M., Chiu W., Kleywegt G.J. Outcome of the first electron microscopy validation task force meeting. Structure 2012, 20:205-214.
19. Heymann J.B., Cardone G., Winkler D.C., Steven A.C. Computational resources for cryo-electron tomography in Bsoft. J. Struct. Biol. 2008, 16:232-242.
20. Hill E. Announcing the JCB Data Viewer, a browser-based application for viewing original image files. J. Cell Biol. 2008, 183:969-970.
21. Jones T.A., Zou J.-Y., Cowan S.W., Kjeldgaard M. Improved methods for the building of protein models in electron density maps and the location of errors in these models. Acta Crystallogr. 1991, A47:110-119.
22. Kantardjieff K.A., Rupp B. Matthews coefficient probabilities: improved estimates for unit cell contents of proteins, DNA, and protein-nucleic acid complex crystals. Protein Sci. 2003, 12:1865-1871.
23. Kinjo A.R., Suzuki H., Yamashita R., Ikegawa Y., Kodou T., Igarashi R., Kengaku Y., Cho H., Standley D.M., Nakagawa A., Nakamura H. Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format. Nucleic Acids Res. 2012, 40(D1):D453-D460.
24. Lawson C.L., Baker M.L., Best C., Bi C., Dougherty M., Feng P., van Ginkel G., Devkota B., Lagerstedt I., Ludtke S.J., Newman R.H., Oldfield T.J., Rees I., Sahni G., Sala R., Velankar S., Warren J., Westbrook J.D., Henrick K., Kleywegt G.J., Berman H.M., Chiu W. EMDataBank.org: unified data resource for CryoEM. Nucleic Acids Res. 2011, 39:D456-D464.
25. Liu H., Jin L., Koh S.B.S., Atanasov I., Schein S., Wu L., Zhou Z.H. Atomic structure of human adenovirus by Cryo-EM reveals interactions among protein networks. Science 2010, 329:1038-1043.
26. Lorensen W.E., Cline H.E. Marching cubes: a high resolution 3D surface construction algorithm. Comput. Graph. (ACM) 1987, 21:163-169.
27. Macias J.R., Jimenez-Lozano N., Carazo J.M. Integrating electron microscopy information into existing Distributed Annotation Systems. J. Struct. Biol. 2007, 158:205-213.
28. Nemecek D., Cheng N., Qiao J., Mindich L., Steven A.C., Heymann J.B. Stepwise expansion of the bacteriophage φ6 procapsid: possible packaging intermediates. J. Mol. Biol. 2011, 414:260-271.
29. Orloff D.N., Iwasa J.H., Martone M.E., Ellisman M.H., Kane C.M. The cell: an image library-CCDB: a curated repository of microscopy data. Nucleic Acids Res. 2013, 41:D1241-D1250.
30. Patwardhan A., Carazo J.-M., Carragher B., Henderson R., Heymann J.B., Hill E., Jensen G.J., Lagerstedt I., Lawson C.L., Ludtke S.J., Mastronarde D., Moore W.J., Roseman A., Rosenthal P., Sorzano C.-O.S., Sanz-García E., Scheres S.H.W., Subramaniam S., Westbrook J., Winn M., Swedlow J.R., Kleywegt G.J. Data management challenges in three-dimensional EM. Nat. Struct. Mol. Biol. 2012, 19:1203-1207.
31. Pettersen E.F., Goddard T.D., Huang C.C., Couch G.S., Greenblatt D.M., Meng E.C., Ferrin T.E. UCSF Chimera - a visualization system for exploratory research and analysis. J. Comput. Chem. 2004, 25:1605-1612.
32. Saijo H., Shiojiri M. Ultra-fast spectrometric cathodoluminescence scanning microscopy for materials analysis. Mater. Trans. 2010, 51:231-236.
33. Stinchcombe J.C., Majorovits E., Bossi G., Fuller S., Griffiths G.M. Centrosome polarization delivers secretory granules to the immunological synapse. Nature 2006, 443:462-465.
34. Tagari M., Newman R., Chagoyen M., Carazo J.-M., Henrick K. New electron microscopy database and deposition system. Trends Biochem. Sci. 2002, 27:589.
35. The Gene Ontology Consortium Gene ontology: tool for unification of biology. Nat. Genet. 2000, 25:25-29.
36. The UniProt Consortium Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2012, 40:D71-D75.
37. Velankar S., Kleywegt G.J. The Protein Data Bank in Europe (PDBe): bringing structure to biology. Acta Crystallogr. D 2011, 67:324-330.
38. Velankar S., Best C., Beuth B., Boutselakis C.H., Cobley N., Sousa da Silva A.W., Dimitropoulos D., Golovin A., Hirshberg M., John M., Krissinel E.B., Newman R., Oldfield T., Pajon A., Penkett C.J., Pineda-Castillo J., Sahni G., Sen S., Slowley R., Suarez-Uruena A., Swaminathan J., van Ginkel G., Vranken W.F., Henrick K., Kleywegt G.J. PDBe: Protein Data Bank in Europe. Nucleic Acids Res. 2010, 38:D308-D317.
39. Velankar S., Alhroub Y., Alili A., Best C., Boutselakis H.C., Caboche S., Conroy M.J., Dana J.M., van Ginkel G., Golovin A., Gore S.P., Gutmanas A., Haslam P., Hirshberg M., John M., Lagerstedt I., Mir S., Newman L.E., Oldfield T.J., Penkett C.J., Pineda-Castillo J., Rinaldi L., Sahni G., Sawka G., Sen S., Slowley R., Sousa da Silva A.W., Suarez-Uruena A., Swaminathan G.J., Symmons M.F., Vranken W.F., Wainwright M., Kleywegt G.J. PDBe: Protein Data Bank in Europe. Nucleic Acids Res. 2011, 39:D402-D410.
40. Velankar S., Alhroub Y., Best C., Caboche S., Conroy M.J., Dana J.M., Fernandez Montecelo M.A., van Ginkel G., Golovin A., Gore S.P., Gutmanas A., Haslam P., Hendrickx P.S.M., Heuson E., Hirschberg M., John M., Lagerstedt I., Mir S., Newman L.E., Oldfield T.J., Patwardhan A., Rinaldi L., Sahni G., Sanz Garcia E., Sen S., Slowley R., Suarez-Uruena A., Swaminathan G.J., Symmons M.F., Vranken V.F., Wainwright M., Kleywegt G.J. PDBe: Protein Data Bank in Europe. Nucleic Acids Res. 2012, 40:D445-D452.
41. Voronoi G. Nouvelles applications des paramètres continus à la théorie de formes quadratiques. Journal für die reine und angewandte Mathematik 1908, 133:97-178.
42. Yokoyama T., Shaikh T.R., Iwakura N., Kaji H., Kaji A., Agrawal R.K. Structural insights into initial and intermediate steps of the ribosome recycling process. EMBO J. 2012, 31:1836-1846.
43. Zhang R., Hryc C.F., Cong Y., Liu X., Jakana J., Gorchakov R., Baker M.L., Weaver S.C., Chiu W. 4.4 Angstrom cryo-EM structure of an enveloped alphavirus venezuelan equine encephalitis virus. EMBO J. 2011, 30:3854-3863.
44. Zhang X.Z., Sun S., Xiang Y., Wong J., Klose T., Raoult D., Rossmann M.G. Structure of sputnik, a virophage, at 3.5-A resolution. Proc. Natl. Acad. Sci. USA 2012, 109:18431-18436.