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Depositing Data in Repositories: PDB

How to submit to PDB

Image credit: RCSB PDB

Before submitting

Before depositing 

  1. Prepare data 

  • Data extraction tools 

    • pdb_extract: Extract and harvest data in PDBx/mmCIF format from structure determination programs 

    • SF-Tool : Convert structure factor files among various formats 

  • Data format conversion tools 

    • PDBML2CIF: Convert PDBML-format data into PDBx/mmCIF-format 

    • PointSuite: Generate symmetry records for macromolecular assemblies with point and helical symmetries 

    • MAXIT: Translate data between file formats and more 

  1. Validate data 

  • Validate your data prior to deposition using the wwPDB validation system, a standalone server that performs the same validation as you would observe during the deposition process 

  • The wwPDB Validation Task Forces develop validation reports to assess the quality of a structure and highlight specific concerns by considering the coordinates of the model. Easily interpretable summary information that compares the quality of a model with that of other models in the archive will help users of PDB data to critically assess archived entries and to select the most appropriate structural models for their needs. 

  • Information and example Validation Reports 

Submission steps

To deposit: All depositions in PDB are made through OneDep 

  1. Log in or create a OneDep account. This can be done by creating a OneDep ID, or by using your ORCID ID. PDB recommends using ORCID when possible. 

  1. Create a new session by entering your email address into the field on the left-side bar. This does not need to be the same address you use for your ORCID account even if you logged into OneDep via ORCID 

  1. Click the link sent to your email, which will redirect you back to OneDep 

  1. Select your country from the drop-down menu  

  1. Fill in the deposition form (keep in mind that your deposition password is autogenerated and will be sent to you via email after filling out the form) 

  1. Click “start deposition” 

  1. A new deposition session will be added to your account summary table; you can access the session by clicking the deposition ID 

  1. Select the "File upload" option from the left-hand navigation panel to upload coordinate and structure factor files (for X-ray structures). Once the files have been uploaded, select the corresponding file types from the drop-down menus. 

  1. After file upload has been initiated, initial validation calculations begin. The depositor will receive an e-mail notification when validation has completed. Once validation is complete, validation reports are available for review under "Validation Reports" at the bottom of the navigation panel. 

  1. It is strongly recommended that you review the "Upload Summary" page carefully as it indicates which data have been uploaded and interpreted correctly 

  1. Use the left-side bar to navigate between and complete the data entry pages. As you enter data, the list of minimum mandatory items required for submission is automatically checked by the system. In the left-hand navigation panel, two bars indicate the percentage of completeness of the deposition: 

  • The Submit button is shaded by the percentage of mandatory data items submitted. Clicking on this bar will provide a list of the missing mandatory items. The entry can be submitted when the button is completely green. 

  • The Data Supplied button is shaded by the percentage of all possible data items that have been provided. 

  1. Sequence and ligand information should be reviewed in the “Macromolecules” folder and the “Ligands” page, respectively 

  1. Coordinate and experimental data files can be replaced at any time prior to submission using the "Replacement Upload" page available from the navigation panel. 

  1. The "Communication" page available from the navigation panel should be used for all correspondence with the wwPDB. This page will store all messages related to the deposition. 

  1. Prior to submission, you must agree to the Terms and Conditions listed on the "Summary & conditions" page. 

  1.  You will also be asked to review the initial validation report available on the "Validation Reports" page and indicate your acceptance. 

  1. Once all mandatory items have been captured (all pages show green check marks on the navigation menu) the "Submit deposition" button in the top left corner will become completely green to indicate that the entry can be submitted. 

  1. Processed files and validation reports sent by PDB biocuration staff will be available for download and review on the "Communication" page.