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Deposition

Deposition. http://www.ebi.ac.uk/msd-srv/emdep. 3DEM WORKFLOW PIPELINE. BIOCHEMICAL SAMPLE. SPECIMEN PREPARATION. IMAGING. ELECTRONIC NOTEBOOK. ELECTRONIC NOTEBOOK. MICROSCOPE FILM/CCD. MAP-FITTING. IMAGE PROCESSING. RECONSTRUCTION. MAP FITTING SOFTWARE. 3D RECON- STRUCTION

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Deposition

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

  2. 3DEM WORKFLOW PIPELINE BIOCHEMICAL SAMPLE SPECIMEN PREPARATION IMAGING ELECTRONIC NOTEBOOK ELECTRONIC NOTEBOOK MICROSCOPE FILM/CCD MAP-FITTING IMAGE PROCESSING RECONSTRUCTION MAP FITTING SOFTWARE 3D RECON- STRUCTION SOFTWARE SCANS PARTICLE – PICKING

  3. EM Biological Sample Biochemical Preparation EM Specimen Preparation EM Data Collection Image Processing Structure Analysis Biological Sample em_assembly em_entity_assembly em_entity_assembly_list em_virus_entity em_icos_virus_shells

  4. Growth of EM Entries

  5. Database content 3D-EM map Metadescriptors Data files • Optional • Mandatory 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 Figures Slices Masks

  6. 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

  7. Biological Sample Biochemical Preparation EM Specimen Preparation EM Data Collection Image Processing Structure Analysis Textual Descriptors

  8. EM Deposition INTERACTIVE DEPOSITION SYSTEM: 13 DEPOSITION PAGES 120 DATA ITEMS INFORMATION AND HELP ON PAGE UPLOADED FILES 'BASED ON' FACILITY

  9. Sample Details Page

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

  11. SINGLE PARTICLES ICOSAHEDRAL VIRUSES TOMOGRAPHY HELICAL ASSEMBLIES 2D-CRYSTALS EM Deposition Data EM DATA FROM METHODOLOGIES INCLUDING:

  12. Demonstration

  13. Worldwide Protein Data Bank www.wwpdb.org

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

  15. Next slides only to be used if demo fails

  16. Title author

  17. Sample components

  18. Sample components

  19. Single Particle

  20. Individual Structure (Tomogram)

  21. 2d/3d crystal

  22. icosahedral

  23. helical

  24. 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.

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