Deposition

BIOCHEMICAL SAMPLE SPECIMEN PREPARATIONIMAGING IMAGE PROCESSING RECONSTRUCTION MAP-FITTING ELECTRONIC NOTEBOOK MICROSCOPE FILM/CCD ELECTRONIC NOTEBOOK SCANS PARTICLE – PICKING 3D RECON- STRUCTION SOFTWARE MAP FITTING SOFTWARE 3DEM WORKFLOW PIPELINE

EM Data Collection Structure Analysis Image Processing EM Specimen Preparation 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 em_assembly em_entity_assembly em_entity_assembly_list em_icos_virus_shells em_virus_entity

Growth of EM Entries

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 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 Bank

Proposed Method for Depositing and Retrieving EM Data Integrated RCSB deposition system Integrated MSD deposition system EBI RCSB map and fitted coordinate FTP repository EM map/model assessment, visualization and analysis tools MSD Database RCSB Database Electron Microscopy Access Portal Combined Dictionary for Map and Coordinate Data

Next slides only to be used if demo fails

Title author

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