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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
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
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
INTERACTIVE DEPOSITION SYSTEM:
13 DEPOSITION PAGES 120 DATA ITEMS INFORMATION AND HELP ON PAGE UPLOADED FILES 'BASED ON' FACILITY
EMDB Experimental Types
SINGLE PARTICLES ICOSAHEDRAL VIRUSES TOMOGRAPHY HELICAL ASSEMBLIES 2D-CRYSTALS
EM DATA FROM METHODOLOGIES INCLUDING:
SINGLE PARTICLE RECONSTRUCTION
MAP:REPLICATIVE HELICASE DNAB-DNA COMPLEX
RESOLUTION: 26 ANG
MAP SIZE: 8.3 Mb
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/
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