Diamond hits 10,000 structures in the Protein Data Bank

This week, Diamond and its scientific users achieved a significant milestone by depositing its 10,000^th Macromolecular Crystallography (MX) structure in the Protein Data Bank (PDB), a global repository and resource for students and researchers working to understand the molecules of life. This highlights Diamond’s position as one of the most successful and prolific light sources solving biological structures and sharing this information worldwide.

Diamond has a suite of instruments dedicated to solving the 3D structure of large biological molecules – proteins, DNA and RNA. Scientists use the MX beamlines to reveal the shape and arrangement of biological molecules at atomic resolution, knowledge of which provides a highly accurate insight into function.  Each 3D structure solved is deposited into the Protein Data Bank (PDB). The depositions are then released on a weekly basis. Today’s PDB release takes Diamond beyond 10,000 structures deposited.

Dr Dave Hall, MX Science Group Leader at Diamond, says:

Professor Dave Stuart, Director of Life Sciences at Diamond Light Source and Joint Head of Structural Biology at University of Oxford, comments on the batch of Diamond MX structures released this week, which includes the 10,000^th:

Diamond is one of around 50 synchrotron light source facilities currently in operation worldwide and plays a key role in solving biological structures. In 2019, 35% of all structures solved at synchrotrons in Europe were solved at Diamond and around 11% of all worldwide synchrotron structures were solved at Diamond. The detailed structural information is extremely valuable for instance in drug design. This is illustrated aptly by a 2017 economic analysis performed by the Rutgers Office of Research Analytics which noted that a reasonable estimate to replicate the PDB data archive at the time was $12 billion*.

* Economic Impacts of the Research Collaboratory for Structural Bioinformatics (RCSB)Protein Data Bank, May 2017. https://www.rcsb.org/pages/about-us/economic-impact

Overall structure of xcis-PT, one of the structures solved at Diamond Light Source released in the PDB this week, taking Diamond over 10,000 depositions. Solving the structure of xcis-PT – a human prenyltransferase composed of a tetrameric assembly of two proteins – was key to understanding certain enzymatic mutations that can lead to severe human diseases. Mutations in either or both proteins that form the tetramer have been linked with retinitis pigmentosa, epilepsy, visual, neurological and hearing impairments to name a few. From: Structural basis of heterotetrameric assembly and disease mutations in the human cis-prenyltransferase complex (Nature Communications, DOI: 10.1038/s41467-020-18970-z).

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