Deposition

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

BIOCHEMICALSAMPLE

SPECIMENPREPARATION IMAGING

IMAGEPROCESSINGRECONSTRUCTION

MAP-FITTING

ELECTRONICNOTEBOOK

MICROSCOPEFILM/CCD

ELECTRONICNOTEBOOK

SCANSPARTICLE –

PICKING

3D RECON-STRUCTIONSOFTWARE

MAP FITTINGSOFTWARE

3DEM WORKFLOW PIPELINE

EM Data Collection

Structure AnalysisImage Processing

EM SpecimenPreparation

Biochemical Preparation

EM

em_assembly

_em_assembly.id

_em_assembly.entry_id

_em_assembly.name

_em_assembly.aggregation_state

_em_assembly.composition

_em_assembly.num_components

_em_assembly.mol_wt_exp

_em_assembly.mol_wt_theo

_em_assembly.mol_wt_method

_em_assembly.details

Biological Sample

Biological Sample

em_assembly

em_entity_assembly

em_entity_assembly_list

em_icos_virus_shells

em_virus_entity

Growth of EM Entries

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

Database content

Figures

Slices

Masks

3D-EM Deposited Data

MANDATORY: 3D- EM MAPS

TEXTUAL DESCRIPTORS

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

Textual Descriptors

EM Deposition

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

EM Deposition Data

SINGLE PARTICLES ICOSAHEDRAL VIRUSES TOMOGRAPHY HELICAL ASSEMBLIES 2D-CRYSTALS

EM DATA FROM METHODOLOGIES INCLUDING:

Demonstration

Worldwide Protein Data Bankwww.wwpdb.org

Proposed Method for Depositing and Retrieving EM Data

IntegratedRCSB deposition

system

IntegratedMSD deposition

system

EB

IR

CS

B

map and fitted coordinateFTP repository

EM map/model assessment, visualization

and analysis tools

MSDDatabase

RCSBDatabase

Electron Microscopy Access Portal

Combined Dictionary for Map and Coordinate Data

Next slides only to be used if demo fails

Title author

Sample components

Sample components

Single Particle

Individual Structure (Tomogram)

2d/3d crystal

icosahedral

helical

TO FINALLY DEPOSIT THE ENTRY:

click on ‘GET ACCESSION NUMBER’ button (upper left).

You will receive by email an ‘ACCESSION’ number for your entry (eg EMD-1234) which can be used in EMsearch to link to the atlas pages for your entry.