Data Deposition and Release Policies

The RCSB PDB follows the policies as determined and outlined by the wwPDB.

Data Deposition

PDB depositions are restricted to atomic coordinates that are substantially determined by experimental measurements on specimens containing biological macromolecules.

PDB depositions include: polypeptide structures containing 24 or more residues; smaller peptides complexed with a polymer greater than 24 residues; polynucleotide structures with 4 or more residues; coordinates for the repeating unit of fibrous polymers; and polysaccharide structures with 4 or more sugar residues.

Molecules that do not conform to these guidelines but have been previously deposited in the PDB will not be removed. Crystal structures of peptides with fewer than 24 residues, such as antibiotics, should be sent to the Cambridge Crystallographic Data Centre (CCDC). NMR structures with small peptides smaller than 24 residues should be submitted to the SMSdep server at BMRB. Smaller oligonucleotides (dinucleotides and trinucleotides) can be deposited at the Nucleic Acid Database (NDB).

In addition to coordinate data, structure factor amplitudes/intensities (for crystal structures) and restraints (for NMR structures) are required for PDB deposition.

Coordinate and Experimental Data Release

The length of time that a structure is held from public release is selected during deposition: Hold for 8 Weeks, Hold for 6 Months, Hold for 1 Year, Hold for Publication, or Release Now.

The maximum hold period is one year, even if the corresponding paper has not been published. Depositors will be given the option to either release or withdraw the deposition at that time.

Holding for a defined period of time (HOLD)

Structures placed on "hold" are automatically released at the expiration of the hold period. There is a one-year hold limit.

Hold For Publication (HPUB)

The status HPUB indicates that a structure will be released when the corresponding journal article is published electronically or in print. There is a one-year hold limit.

The wwPDB receives publication information from some journals, and automatically searches for new publications. We encourage sending citation updates to deposit@deposit.rcsb.org.

Release Now (REL)

Structures will be released as soon as processing is complete.

Sequence Pre-release

Depositors can release the primary sequence in advance of the coordinates. ADIT's default setting is set to (REL), meaning sequence pre-release.

Sequence pre-release can prevent unintended duplication of effort in structure determination, and allow users to conduct blind tests of structure prediction and modeling techniques.

Pre-released sequences can be viewed using the Unreleased Entries search form.

Release Schedule

The PDB archive is updated by 4:00 EST each Wednesday. For a structure to be released as part of that update, release requests containing the PDB ID and related publication information should be sent to deposit@deposit.rcsb.org by 12:00 noon EST on the preceding Thursday. Requests received after this cutoff time will be processed during the next update cycle.

Each week, all files scheduled for release or modification are checked and validated one final time. Authors may be contacted to resolve any issues that may arise while preparing the entries for release. If this is not accomplished within that release cycle, the entry may be scheduled for released in a later update.

Additional Information

A document about Frequently Asked Questions About Depositing, Updating and Releasing Files is available. [Click here]

Last Updated: May 6, 2008

Questions, comments, and suggestions should be sent to deposit@deposit.rcsb.org.