Exploring a 3D Structure
What are Versions?
The PDB archives experimental data and coordinates of all polymeric and small molecules included in the structure. The structures represent a specific chemical and structural state of the biological molecule(s) included in the experiment. The structural coordinates and related chemical information deposited by the authors are the primary data, while metadata such as the protein name, who solved the structure, experimental details, literature information, etc. are secondary data.
The first release of a PDB entry with a specific PDB identifier is called version 1 of the structure. Any set of changes to the metadata is considered a minor revision and the updated version of the file is assigned a number with an increment of 0.1 to the last version of the entry. Any change that impacts the chemistry and or coordinates of all or parts of the structure is considered a major revision and the version number is incremented by +1. Learn more about versions of PDB entries.
Why have Versions?
PDB entries (experimental data, coordinates, and metadata) are downloaded by many data resources and research facilities for purposes of analysis, visualization, and more. PDB ID and links to PDB the entries are listed in the literature, educational materials, and other data resources. Changing the PDB ID every time any change or correction is made to the PDB entry would be confusing for users. For that reason, a corrected entry is instead updated with the same PDB identifier and a new version number.
In order to inform all users that changes have been made to an entry since it was last released, the updated entry with a new version number is re-released during the next weekly update. This alerts automated scripts and pipelines that download entry files from the PDB to save the updated version of the file for use. The older version of the entry is also made available for download, both for reference and for use in education, etc. The numbered versioning allows users to track which changes were included in the latest version and why those changes were made. This knowledge can help users make informed decisions about use of the entry in research and education.
The Structure Summary page provides a short summary of the versions of a PDB entry and the reasons for the changes. On the Versions page the complete history is recorded with options to download all versions of the entry that follow Major revisions.
The version history is presented in a tabular format as shown in Figure 1. It includes the version number, versioning date, type and reason for re-releasing (versioning) the entry, changes made and the mmCIF categories affected by the changes.
The latest version of each entry file is available for download from the Structure Summary and related pages. Older versions of the files can be downloaded from the table on the Versions Tab.
|Figure 1. Tabular representation of the version history of the PDB entry 6m17 (as of October 2021).
Learning about the Structure
The following things can be learned about the PDB ID 6m17 structure from the versions history (see Figure 1):
- In versions 1.1 through 1.5 of the structure, minor changes were made in specifying the biological assembly, database references, source of protein, etc. These changes do not impact the chemical and structural information of any part of the structure.
- Version 2.0 involved changes to the coordinates of the structure. These changes were related to the carbohydrate remediation of the archive. Since the proteins in this entry are glycosylated, representation of sugars in the entry was updated to match the current standards.
- Version 3.0 of the entry was released with an author-provided coordinate replacement to improve and correct the structure. Following this, the protein name(s) were updated in version 3.1