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EMDB Richard Newman Monica Chagoyen Mohamed Tagari

EMBL-EBI. EMDB Richard Newman Monica Chagoyen Mohamed Tagari. Cryo-Electron Microscopy Structure Deposition Workshop RCSB Protein Data Bank in Rutgers University , Piscataway, NJ Saturday October 23, 2004 to Sunday October 24, 2004. Kim Henrick. http://www.ebi.ac.uk/msd/projects/IIMS.html.

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EMDB Richard Newman Monica Chagoyen Mohamed Tagari

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  1. EMBL-EBI EMDBRichard NewmanMonica ChagoyenMohamed Tagari Cryo-Electron Microscopy Structure Deposition Workshop RCSB Protein Data Bank in Rutgers University, Piscataway, NJ Saturday October 23, 2004 to Sunday October 24, 2004. Kim Henrick

  2. http://www.ebi.ac.uk/msd/projects/IIMS.html http://www.biochem.mpg.de/eu/3DEMwebsite/index_3dem.html

  3. EM – Collection of Ideas

  4. Common Conventions for Interchange and Archiving of Electron Microscopy Information in Structural Biology David Belnap Laboratory of Structural Biology Research, NIAMS National Institutes of Health Bethesda, Maryland, USA Monica Chagoyen Centro Nacional de Biotecnologia Madrid, Spain

  5. http://www.iplt.org/doc/html/standards.html Iplt—image processing library and toolkit for the electron microscopy community Ansgar Philippsen, Andreas D. Schenk, Henning Stahlberg and Andreas Engel Maurice Müller Institute for Structural Biology, Biozentrum, Klingelbergstr. 70, 4056, Basel, Switzerland

  6. Steve Ludtke, Laurie Nason, Haili Tu, Liwei Peng, Wah Chiu Object oriented Database and Electronic Notebook for Electron Cryomicroscopy National Center for Macromolecular Imaging Baylor College of Medicine Jianlin Lei, Yu Chen, Bill Baxter, Dean Leith, Bob Grassucci, Joachim Frank Methods and technologies for data flow from EM acquisition to completed reconstruction - including automated microscopy, reconstruction engine, and project archiving Computational Biology & Molecular Imaging Wadsworth Center, Albany, NY, USA

  7. EM • EMDB – Database Model • Emdep – Deposition System • Access via WWW Emsearch/Atlas pages • Access via FTPdownload • Fitted Coordinates and the PDB

  8. Single-particle cryo-EM by angular reconstitution

  9. IMAGE RECORDING PARAMETERS MICROSCOPE PARAMETERS DIGITISATION PARAMETERS PARTICLE PICKING CTF CORRECTION CHARACTERISTIC VIEWS RESOLUTION DETERMINATION RECONSTRUCTION METHOD FITTING ATOMIC COORDS METHOD VOLUME MAP Single-particle cryo-EM by angular reconstitution LABORATORY NOTEBOOK/ COMPUTER TEXT

  10. EMDB content 3D-EM map Metadescriptors Data files • Optional • Mandatory Release: immediate Title: “The Structure of the Semliki Forest Virus at 9 Å resolution” Authors: E. Mancini M. Clarke B. E. Gowen T. Rutten S. D. Fuller Reference paper: Mol Cell (2000) 5, 255 Complex Name: Semliki Forest Virus SFV Aggregation: icosahedral Describe composition: partial Components Name: spike glycoprotein E1 spike glycoprotein E2 spike glycoprotein E3 coat protein C Type: protein Source: natural Source organism: Semliki Forest Virus Experiment Microscope: TEM Temperature range: liquid nitrogen Reconstruction method: fourier-bessel Figures Slices Masks

  11. EMDB Deposited Data MANDATORY: • 3D- EM MAPS • META DATA OPTIONAL ADDITIONAL DATA FILES: • MASKS • SUPPLEMENTARY FIGURES • ORTHOGONAL MAP SLICES • STRUCTURE FACTORS • FSC .xml FILE • LAYER-LINE DATA

  12. Biological Sample Biochemical Preparation EM Specimen Preparation EM Data Collection Image Processing Structure Analysis Meta Data

  13. Example:Vitrification DATA ITEM ELEMENTS: eg PARENT:VITRIFICATION “vitrify_type” CHILD:CRYOGEN NAME “cryogen_name” <xs:complexType name="vitrifType"> <xs:sequence> <xs:element name="cryogen_name" type="xs:string"/> <xs:element name="humidity" type="xs:string"/> <xs:element name="temperature" type="emd:tempType"/> <xs:element name="instrument" type="xs:string"/> <xs:element name="method" type="xs:string"/> <xs:element name="time_resolved_state" type="xs:string"/> <xs:element name="details" type="xs:string"/> <xs:element name="citation" type="emd:pubType"/> </xs:sequence>

  14. EMDEP http://www.ebi.ac.uk/msd-srv/emdep

  15. EMDEP INTERACTIVE DEPOSITION SYSTEM: • 13 DEPOSITION PAGES • 120 DATA ITEMS • INFORMATION AND HELP ON PAGE • UPLOADED FILES • 'BASED ON' FACILITY

  16. Sample Details Page

  17. XML data automatically Filled in by software Reading map headers MAPS em2em – CCP4

  18. EMDB Experimental Types • SINGLE PARTICLES • ICOSAHEDRAL VIRUSES • TOMOGRAPHY • HELICAL ASSEMBLIES • 2D-CRYSTALS EM DATA FROM METHODOLOGIES INCLUDING:

  19. ICOSAHEDRAL RECONSTRUCTION MAP:BACTERIOPHAGE PRD1 CAPSID RESOLUTION:~14 ANG MAP SIZE:8.3 Mb

  20. SINGLE PARTICLE RECONSTRUCTION MAP:REPLICATIVE HELICASE DNAB-DNA COMPLEX RESOLUTION:26 ANG MAP SIZE:8.3 Mb

  21. TOMOGRAPHIC RECONSTRUCTION MAP:INSECT FLIGHT MUSCLE RESOLUTION:~40 ANG MAP SIZE:42.3 Mb

  22. EM SEARCH http://www.ebi.ac.uk/msd-srv/emsearch

  23. EM-Search: Index Page

  24. EM-Search: Results Page

  25. Atlas Page: Summary

  26. FTP ACCESS ftp://ftp.ebi.ac.uk/pub/databases/emdb/ • XML Header files available after deposition, curation and approval by author (no HOLD) • Data Files (may have HOLD period) for • 3D- MAP • Masks • Figures • Orthogonal map slices • Structure factors • Layer- line data

  27. Bacteriophage T4 baseplate Kostyuchenko et al., Nat. Struct. Biol.,2003 10, 688 Emd Entry 1048

  28. gp5/gp27 hexamer Bacteriophage T4 PDB Entry 1K28 BACTERIOPHAGE T4 CELL-PUNCTURING DEVICE KANAMARU, et.al., Bacteriophage T4, expressed in Escherichia coli

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