NMR data deposition


Deposition of NMR structures and data at PDBe

This short introduction describes the most convenient way to deposit your NMR data at PDBe: from a CCPN project. If you do not have a CCPN project, you can preferably create one with from your NMR data as mentioned below or submit individual files at the time of deposition, as explained in the section on AutoDep. The figure below shows an overview of the CCPN deposition system together with the 8 numbered steps that are used throughout this overview.

The CCPN project deposition system.
The numbered steps are described in detail in the text below.
  1. In order to use the deposition system, a CCPN project, made with CcpNmr software, is required (see below).
  2. Use CcpNmr ECI (Entry Completion Interface) to add an "Entry" object. Also, edit the data you wish to submit for public use.
  3. For depositions with macromolecular structures, you first submit your CCPN project to the CCPN-AutoDep server at the EBI.
  4. Once this submission is complete, the structural data will be curated by PDBe annotators at the EBI; after this, the depositor will get a PDB ID.
  5. The curated data will then be incorporated back into the submitted CCPN project.
  6. The updated CCPN project will then be saved as an NMR-STAR file.
  7. This NMR-STAR file will then be automatically submitted for you to the ADIT-NMR server at BMRB; at this point, the depositor will be supplied with a link for them to complete the submission at BMRB.
  8. Finally, on completion of this submission, the depositor will get a BMRB ID and the NMR data will be curated by annotators at the BMRB.

Preparing your CCPN project (step 1)

There are two basic ways in which you can get a CCPN project:

  • You already use the CcpNmr Analysis software for analysing your NMR data. In this case, analysis will already be saving your data each time in a CCPN project.
  • You are using other standard NMR packages to analyse your NMR data. In this case, you can read your NMR data (and any structural data) into a CCPN project using the FormatConverter software.

In the first case, you may also have other data in different formats that needs to be submitted with your CCPN project deposition. In this case, you can import the additional data into your existing CCPN project using FormatConverter. It has also recently become possible to use Extend-NMR software to make CCPN projects.

Adding an "Entry" object (step 2)

You may not wish to deposit all the data in your CCPN project - perhaps not all of it is relevant (such as initial structure generations) or some of it may not yet be published and so you wish to keep this data as private for a future publication. For these reasons, it is necessary to add what is called an "Entry" object. An "Entry" is basically a subset of the CCPN project, that includes only the data to be used for deposition. It is possible to add this "Entry" object using either the desktop version of FormatConverter or the newly developed Entry Completion Interface (ECI) software.

To add an "Entry" with desktop FormatConverter, Go to the "Other" menu and select the option "Create/edit Entry". If there are no "Entry" objects in your CCPN project, it will ask for a name for your new "Entry". For ECI, see the main ECI page.

Adding additional information (optional step)

Once you have an "Entry" object, you can submit your CCPN project to the PDBe AutoDep server. If you choose to do this, you will still need to add some additional information (also called meta data; such as authors, publications, sample information, etc.) to complete your deposition. This can be done on the AutoDep web server using the HTML forms on those pages. However, it is also possible to add this information prior to submission using the ECI software in a convenient user-friendly manner. You can also add some of this meta data using the desktop version of FormatConverter.

Here is a list of the meta data that needs to be added for depositions to the PDB and/or the BMRB:

  • PDB title
  • PDB keywords
  • Contact people and laboratory addresses
  • Author information
  • Associated publications
  • Software used
  • Macromolecular sequences and chain information
  • Biological sources and experimental sources of macromolecules
  • Sample and sample condition information
  • NMR spectrometers
  • Information about the NMR experiments used to collect your data

Submitting your CCPN project to PDBe (steps 3-5)

Once you have added an "Entry" object to your CCPN project, you can save it as a gzipped tar (.tar.gz) file. With this file, you can submit your project to AutoDep (3). On finishing the deposition, your data will be curated at PDBe (4). After your data has been curated, the original CCPN project will be updated with the new information (5).

Submission of your data to BMRB (steps 6-8)

Your updated CCPN project will be exported to NMR-STAR format (6). This file will then be uploaded automatically for you to the ADIT-NMR server at BMRB (7) for curation there (8).