General Deposition Guide

This guide is updated by EMDB, which informs the updating of the master OneDep deposition guide here.

For Electron Microscopy Volume Map Depositions:

File upload requirements

Upload of the following files is mandatory:

  1. File: Primary map (.mrc or .ccp4 format, depositors may use gzip or bzip2 compression)
    1. Metadata: voxel size and recommended contour level
  2. File: Half maps (as used for FSC calculation; two maps non-identical maps must be uploaded).
    1. Metadata: voxel size and recommended contour level
    2. Half-maps must be uploaded for SPA, STA, and Helical 3DEM depositions
    3. These half-maps should remain unmodified from their original output in the 3D refinement protocol used.
  3. File: Image of the map (500 x 500 pixels in .jpg, .png, etc. format)
    1. The image must be an image of the entries density

Upload of these additional files is encouraged by EMDB:

  1. File: FSC curve supporting the resolution of the primary map derived from the half-maps
    1. Uploaded as XML and output from common 3D reconstruction softwares
  2. File: Additional maps
    1. For example: Maps with varying b-factors, density modification, etc

All of these files are made publicly available upon release of the EMDB entry.

Macromolecules page for EMDB map-only deposition

Depositors are encouraged to provide sample sequence information along with appropriate UniProt and/or GenBank references for map-only depositions. For a map-only deposition (no coordinates provided), sequence information is optional but encouraged.

Sample information for a 3D Electron Microscopy experiment

Information about the sample used in an electron microscopy experiment and about its source(s) is collected in a hierarchical fashion. An example is provided below:

  1. Overall sample description: ribosome
    1. subcomponent: 50S large ribosomal subunit
      1. subcomponent: 5S rRNA
      2. subcomponent: 23S rRNA
      3. subcomponent: SeC6
      4. subcomponent: 50S ribosomal protein L4
    2. subcomponent: 30S small ribosomal subunit
      1. subcomponent: 16S rRNA
      2. subcomponent: eIF2
      3. subcomponent: 30S ribosomal protein S1
      4. subcomponent: 30S ribosomal protein S2

NOTE: Subcomponents can be added and/or deleted as necessary, but deletion of a subcomponent will result in deletion of all child subcomponents (e.g., deletion of b. from the example above will also delete i., ii., iii., and iv.).

Experimental information

There are five sections in the "EM experiment" folder in the deposition interface. Within each of these sections are data items that link to other experimental sections as well as to back to the overall sample description and its subcomponents (see previous section). As such, it is recommended that the overall sample description and any necessary subcomponents be completed prior to the entry of experimental information into the "EM experiment" section. In addition, it is also recommended that the experimental sections be completed sequentially from the top down.

Details regarding each subsection follow. Please note that there are mandatory items in most of the experimental sections that must be filled in before the deposition can be finalized and submitted.

  1. Specimen preparation. This section comprises information regarding sample vitrification, staining, embedding, and shadowing, as well as details about the sample grid and its pretreatment, film support, and crystal formation (where applicable).
  2. Microscopy. This section comprises comprehensive information regarding the microscope(s) used for data collection, including electron source, specimen holder, energy filters, etc., as well as the microscope settings and other parameters used for each imaging session (magnification, defocus, alignment procedure, etc.). Multiple imaging sessions can be included within the deposition interface by clicking the "+" button at the bottom of the "Microscopy" page.
  3. Image recording. This section comprises information about the detector(s) or other device(s) used for image recording, including the both the physical properties of the detector and the manner in which the images were collected, e.g., data handling during and directly after capture, number of images, rate of movie frame collection, etc. As in the "Microscopy" section, the "+" can be used if multiple detectors were used for image recording.
  4. Reconstruction. This section comprises the details of the method or methods used to generate three-dimensional map(s) from two dimensional images, including particle selection, classification, alignment, angular assignment, and reconstruction. Information about multiple reconstructions can be included.
  5. Fitting interpretation. This section is for information about the fitting of pre-existing atomic coordinates and/or ab initio models to the map, if applicable. Multiple fitting instances can be added (by clicking the "+" button at the bottom of the page) and each instance can accommodate multiple starting models if necessary. Additional details that can be provided include software and settings for any model building, fitting, and/or refinement that was used to generate the final model.