EMDB Richard Newman Monica Chagoyen Mohamed Tagari EMBL-EBI Cryo-Electron Microscopy Structure Deposition Workshop RCSB Protein Data Bank in Rutgers University, Piscataway, NJRCSB Protein Data BankRutgers University Saturday October 23, 2004 to Sunday October 24, Kim Henrick

EM – Collection of Ideas

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

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

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

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

Single-particle cryo-EM by angular reconstitution

LABORATORY NOTEBOOK/ COMPUTER TEXT MICROSCOPE PARAMETERS DIGITISATION PARAMETERS CHARACTERISTIC VIEWS RECONSTRUCTION METHOD FITTING ATOMIC COORDS METHOD RESOLUTION DETERMINATION VOLUME MAP PARTICLE PICKING CTF CORRECTION IMAGE RECORDING PARAMETERS

Data files 3D-EM map Metadescriptors 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  Mandatory  Optional EMDB content Figures Slices Masks

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

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

Example:Vitrification DATA ITEM ELEMENTS: eg PARENT: VITRIFICATION “vitrify_type” CHILD: CRYOGEN NAME “cryogen_name”

EMDEP

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

Sample Details Page

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

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

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

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

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

EM SEARCH

EM-Search: Index Page

EM-Search: Results Page

Atlas Page: Summary

FTP ACCESS  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 ftp://ftp.ebi.ac.uk/pub/databases/emdb/

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

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