EMDB

Richard NewmanMonica ChagoyenMohamed Tagari

EMBL-EBI

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

http://www.biochem.mpg.de/eu/3DEMwebsite/index_3dem.html

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 HealthBethesda, Maryland, USA

Monica Chagoyen

Centro Nacional de Biotecnologia

Madrid, Spain

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

Steve Ludtke, Laurie Nason, Haili Tu, Liwei Peng, Wah ChiuObject oriented Database and Electronic Notebook

for Electron CryomicroscopyNational 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 archivingComputational 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

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 filesData files

3D-EM map3D-EM map

MetadescriptorsMetadescriptors

Release: immediateTitle: “The Structure of the Semliki Forest Virus at 9 Å resolution”Authors: E. Mancini M. Clarke B. E. Gowen T. Rutten S. D. FullerReference paper: Mol Cell (2000) 5, 255Complex

Name: Semliki Forest Virus SFVAggregation: icosahedralDescribe composition: partial

ComponentsName:

spike glycoprotein E1spike glycoprotein E2spike glycoprotein E3coat protein C

Type: proteinSource: naturalSource organism: Semliki Forest Virus

ExperimentMicroscope: TEMTemperature range: liquid nitrogenReconstruction method: fourier-bessel

Mandatory

Optional

EMDB content

Figures

Slices

Masks

EMDB Deposited Data

MANDATORY:3D- EM MAPSMETA 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”

<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>

EMDEP

http://www.ebi.ac.uk/msd-srv/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

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

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) for3D- MAPMasksFiguresOrthogonal map slicesStructure factorsLayer- line data

ftp://ftp.ebi.ac.uk/pub/databases/emdb/

Bacteriophage T4 baseplate

Emd Entry 1048

Kostyuchenko et al., Nat. Struct. Biol.,2003 10, 688

Bacteriophage T4

PDB Entry 1K28BACTERIOPHAGE T4 CELL-PUNCTURING DEVICEKANAMARU, et.al.,Bacteriophage T4, expressed in Escherichia coli

gp5/gp27 hexamer