Extension to EMDB Accession Codes

IP
Irina Persikova
Mon, Jul 7, 2025 2:05 PM

Extension to EMDB Accession Codes

The EMDB archive is experiencing near-exponential growth. To support
this rapid expansion, the wwPDB has been working to prepare our systems
for the future and ensure seamless deposition, validation, and
dissemination of data in the years ahead.

As part of this effort, we are announcing an important change:

EMDB IDs will be extended to support up to six digits, allowing for
identifiers such as EMD-123456. Currently, the archive uses four and
five-digit IDs (e.g., EMD-0123, EMD-45678), with support for identifiers
up to the EMDB ID: EMD-99999. The change to six-digits will increase our
capacity ten-fold and ensure ID availability into the next decade, up to
EMD-999999.

We do not anticipate surpassing 99,999 released entries until around
2028, however, we expect to begin assigning six-digit EMDB IDs sometime
in 2026. As such, as early as 2026, depositors should anticipate being
assigned six-digit IDs within the wwPDB OneDep deposition system, and
the user and developer community can expect six-digit EMDB IDs in the
EMDB archive.

We appreciate your support as the archive grows and thank you for your
contribution to the worldwide effort to archive structural biology data.
We remain committed to ensuring a stable, sustainable and scalable
infrastructure that supports the continued successes and productivity of
the scientific community using structural biology and cryoEM in their
research. For questions or feedback, contact the EMDB team at
emdbhelp@ebi.ac.uk.

Please find the full news here:
https://www.wwpdb.org/news/news?year=2025#68596acb26cf5ddd37333796

On behalf of the wwPDB

--
IRINA PERSIKOVA, Ph.D.
Deputy Biocuration Lead, RCSB Protein Data Bank
Research Associate, Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Road, Piscataway NJ 08854
P: 848.445.4938 | E: irina.persikova@rcsb.org
mailto:irina.persikova@rcsb.org
rcsb.org <www.rcsb.org> | iqb.rutgers.edu http://iqb.rutgers.edu |
facebook https://www.facebook.com/RCSBPDB | twitter
https://twitter.com/buildmodels

Extension to EMDB Accession Codes The EMDB archive is experiencing near-exponential growth. To support this rapid expansion, the wwPDB has been working to prepare our systems for the future and ensure seamless deposition, validation, and dissemination of data in the years ahead. As part of this effort, we are announcing an important change: EMDB IDs will be extended to support up to six digits, allowing for identifiers such as EMD-123456. Currently, the archive uses four and five-digit IDs (e.g., EMD-0123, EMD-45678), with support for identifiers up to the EMDB ID: EMD-99999. The change to six-digits will increase our capacity ten-fold and ensure ID availability into the next decade, up to EMD-999999. We do not anticipate surpassing 99,999 released entries until around 2028, however, we expect to begin assigning six-digit EMDB IDs sometime in 2026. As such, as early as 2026, depositors should anticipate being assigned six-digit IDs within the wwPDB OneDep deposition system, and the user and developer community can expect six-digit EMDB IDs in the EMDB archive. We appreciate your support as the archive grows and thank you for your contribution to the worldwide effort to archive structural biology data. We remain committed to ensuring a stable, sustainable and scalable infrastructure that supports the continued successes and productivity of the scientific community using structural biology and cryoEM in their research. For questions or feedback, contact the EMDB team at emdbhelp@ebi.ac.uk. Please find the full news here: https://www.wwpdb.org/news/news?year=2025#68596acb26cf5ddd37333796 On behalf of the wwPDB -- IRINA PERSIKOVA, Ph.D. Deputy Biocuration Lead, RCSB Protein Data Bank Research Associate, Institute for Quantitative Biomedicine Rutgers, The State University of New Jersey 174 Frelinghuysen Road, Piscataway NJ 08854 P: 848.445.4938 | E: irina.persikova@rcsb.org <mailto:irina.persikova@rcsb.org> rcsb.org <www.rcsb.org> | iqb.rutgers.edu <http://iqb.rutgers.edu> | facebook <https://www.facebook.com/RCSBPDB> | twitter <https://twitter.com/buildmodels>