Happy Holidays and New year from the EMDB! Please be advised that the EMDB team will be operating at reduced capacity between December 15th - January 12th. With this in mind we would ask that you be prepared for longer reply times through both our helpdesk system and the OneDep deposition system. well done on a productive 2025, wishing you all the best and we will see you in 2026!
Latest News
3DEM Structure-Map Validation
August 20, 2025
Q-score as a reliability measure for protein, nucleic acid and small-molecule atomic coordinate models derived from 3DEM maps
Grigore Pintilie, Chenghua Shao, Zhe Wang, Brian P Hudson, Justin W Flatt, Michael F Schmid, Kyle L Morris, Stephen K Burley, Wah Chiu. (2025) Acta Cryst D81: 410-422 doi: 10.1107/S2059798325005923
EMBL-EBI Impact Analysis Survey
July 28, 2025
A total of 2,540 respondants took the time to fill in this EMBL-EBI survey. We will learn how EMDB and other services like EMPIAR and PDB help you and this will help EMBL-EBI make the case for why open data resources are critical to life science research. Thank you for the incredible number of responses.
EMDB has officially been elevated to a Core Data Resource by ELIXIR
January 6, 2024
We are delighted to share that EMDB has officially been elevated to a Core Data Resource by ELIXIR, recognising it as a European data resource of fundamental importance to the wider life-science community and the long-term preservation of biological data.
EMDB Nucleic Acids Research paper
November 23, 2023
We are happy to share the most recent version of the EMDB Nucleic Acids Research paper. The paper describes recent developments and future plans of the EMDB in the context of the worldwide Protein Data Bank. Check it out now! https://doi.org/10.1093/nar/gkad1019
EMDB Now Provides Metadata in mmCIF Format
October 4, 2023
We are now providing the metadata for all EMDB entries in mmCIF files as well as the existing XML format! For more details see wwPDB news.
Kyle Morris Appointed New EMDB Team Leader
October 2, 2023
Kyle Morris has joined the EMDB as our new team leader! Kyle brings 10 years of first-hand experience in cryoEM to our team, from his own research, as well as work in imaging and structural biology facilities.
EMICSS: New Cross-Reference Resource for EMDB Entries
December 21, 2022
EMDB proudly announces the EMICSS resource. It provides weekly updated cross-reference information for all EMDB entries to other resources (including PDB, EMPIAR, Europe PMC, UniProt, AlphaFold DB and many more.) Read more here: emdb-empiar.org/emicss.
EMDB Validation Analysis Officially Launched
October 12, 2022
EMDB Validation Analysis (VA) is officially launched at https://www.ebi.ac.uk/emdb/va/. It is available as a local stand-alone package and is coming soon to CCP-EM.
EMDB and EMPIAR Launch YouTube Channel
June 7, 2022
EMDB and EMPIAR have launched a dedicated YouTube channel where you can find talks, tutorials, and much more. Check it out and let us know what content you would like to see.
wwPDB Adopts EMDB Data Model Version 3
February 2, 2022
In February 2022, wwPDB switched to using version 3 of the EMDB data model and the old data model (v1.9.6) is no longer supported. Read the wwPDB announcement for more details.
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Recent Entries
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The local cryo-EM map of CATSPERGamma of Monomer A of the CatSper dimer
The local cryo-EM map of CATSPERBeta of Monomer B of the CatSper dimer
The local cryo-EM map of CATSPERDelta of Monomer A of the CatSper dimer
The local cryo-EM map of the eta-eta interface of the CatSper dimer
The local cryo-EM map of the extracellular region of Monomer A of the CatSper trimer
The local cryo-EM map of the transmembrane region of the CatSper dimer
The local cryo-EM map of CATSPERDelta of Monomer B of the CatSper dimer
Cryo-EM structure of E. coli glycine decarboxylase (P-protein) apo
Cryo-EM structure of RSV pre-F trimer in complex with CNR2056/CNR2047
Cryo-EM structure of RSV pre-F monomer in complex with CNR2056/CNR2047
Cryo-EM structure of RSV pre-F dimer in complex with CNR2056/CNR2047
CryoEM structure of Western equine encephalitis virus California VLP in complex with VLDLR-LA3
GTPBP1*GDP*Phe-tRNA*ribosome in the post-GTP hydrolysis state, Structure IV
GTPBP1*GCP*Phe-tRNA*ribosome in the GTPase activation-like state, Structure III
Cryo-EM structure of a designed pyridoxal phosphate (PLP) synthase fused to a designed circumsporozoite protein antigen from Plasmodium falciparum (CSP-P1-CSP and CSP-P2-CSP)
Constituent EM map: Focused refinement on Ry34 of mouse RyR1 (including auxiliary transmembrane helix TMx; EGTA-only dataset)
Constituent EM map: Focused refinement on BSol of mouse RyR1 (Ca2+/CFF/ATP dataset; closed pore)
Constituent EM map: Focused refinement on JSol+CSol of mouse RyR1 with simvastatin (Ca2+/CFF/ATP dataset; open pore)
Constituent EM map: Focused refinement on Ry34 of mouse RyR1 (Ca2+/CFF/ATP dataset; closed pore)
Constituent EM map: Focused refinement on BSol of mouse RyR1 (including auxiliary transmembrane helix TMx; EGTA-only dataset)
Constituent EM map: Focused refinement on NTD+SPRY+Calstabin-1 of mouse RyR1 (Ca2+/CFF/ATP dataset; closed pore)
Constituent EM map: Focused refinement on Ry34 of mouse RyR1 (Ca2+/CFF/ATP dataset; open pore)
Constituent EM map: Focused refinement on NTD+SPRY+Calstabin-1 of mouse RyR1 (including auxiliary transmembrane helix TMx; EGTA-only dataset)
Constituent EM map: Focused refinement on Ry12 of mouse RyR1 with simvastatin (Ca2+/CFF/ATP dataset; open pore)
Constituent EM map: Focused refinement on Ry34 of mouse RyR1 with simvastatin (Ca2+/CFF/ATP dataset; open pore)
Constituent EM map: Focused refinement on Ry12 of mouse RyR1 (including auxiliary transmembrane helix TMx; EGTA-only dataset)
Constituent EM map: Focused refinement on Ry12 of mouse RyR1 (Ca2+/CFF/ATP dataset; open pore)
Constituent EM map: Focused refinement on JSol+CSol of mouse RyR1 (Ca2+/CFF/ATP dataset; closed pore)
Constituent EM map: Focused refinement on NTD+SPRY+Calstabin-1 of mouse RyR1 (Ca2+/CFF/ATP dataset; open pore)
Constituent EM map: Focused refinement on JSol+CSol of mouse RyR1 (Ca2+/CFF/ATP dataset; open pore)
Constituent EM map: Focused refinement on JSol+CSol of mouse RyR1 (including auxiliary transmembrane helix TMx; EGTA-only dataset)
Constituent EM map: Focused refinement on Ry12 of mouse RyR1 (Ca2+/CFF/ATP dataset; closed pore)
Constituent EM map: Focused refinement on BSol of mouse RyR1 (Ca2+/CFF/ATP dataset; open pore)
Constituent EM map: Focused refinement on NTD+SPRY+Calstabin-1 of mouse RyR1 with simvastatin (Ca2+/CFF/ATP dataset; open pore)
Constituent EM map: Focused refinement on BSol of mouse RyR1 with simvastatin (Ca2+/CFF/ATP dataset; open pore)
Constituent EM map: Focused refinement on Ry34 of mouse RyR1 with simvastatin (Ca2+/CFF/ATP dataset; closed pore)
Constituent EM map: Focused refinement on Ry12 of mouse RyR1 with simvastatin (Ca2+/CFF/ATP dataset; closed pore)
Constituent EM map: Focused refinement on BSol of mouse RyR1 with simvastatin (Ca2+/CFF/ATP dataset; closed pore)
Constituent EM map: Focused refinement on NTD+SPRY+Calstabin-1 of mouse RyR1 with simvastatin (Ca2+/CFF/ATP dataset; closed pore)
Constituent EM map: Focused refinement on JSol+CSol of mouse RyR1 with simvastatin (Ca2+/CFF/ATP dataset; closed pore)
Cryo-EM structure of violaxanthin-chlorophyll-a-binding protein with red shifted Chl a (rVCP) from Trachydiscus minutus at 2.4 angstrom
Cryo-EM structure of the Lhcp trimer from Ostreococcus tauri at 1.94 angstrom resolution
Cryo-EM structure of SARS-CoV-2 spike S2' trimer (dimer of trimer)
Type III-B CRISPR-Cas effector from Archaeoglobus fulgidus (Form 1)
FADD-DED filaments coordinate complex IIa assembly during TNF-induced apoptosis
Type III-B CRISPR-Cas effector from Archaeoglobus fulgidus (Form 2)
cryo-EM structure of RNF20/RNF40-RAD6A-Ub in complex with H2BS112GlcNAc nucleosome
Local refinement of interface of HSV UL5 and UL30 in the replication fork
HIV-1 R18L CA pentamer from capsid-like particles assembled in 1 M NaCl
Focused map of COP9 signalosome deneddylation state with cullin-4A
Cryo-EM structure of post-fusion EBV gB in complex with AMMO2 fab
Cryo-EM structure of Croatia 2023 H3N2 Influenza A hemagglutinin (HA) trimer
CryoEM structure of filament of Bacillus subtilis TIR domain protein SpbK
CryoEM structure of the YonE portal protein from Bacillus phage SPbeta
The PSI3-IsiA43 complex with a closed double ring of IsiA proteins bound to a trimeric PSI core
Structure of beta1-AR-Gs complex bound to epinephrine and an allosteric modulator
The PSI1-IsiA13 complex with double-layered IsiA proteins bound to the monomeric PSI core
Cryo-EM structure of ASFV DNA polymerase in a DNA replication state
Croy-EM structure of HEV_4 p495 virus-like particle in complex with antibody 6H8
Cryo-EM structure of the cytosolic ARMH2-EFCAB9-CATSPERz subcomplex of the mouse CatSpermasome
Gi-bound kappa opioid receptor in complex with dynorphin and positive allosteric modulator MPAM-15
The apo structure (State 1) of African Swine Fever Virus DNA polymerase
Hexamer Msp1 from S.cerevisiae(with a catalytic dead mutation) in complex with an unknown peptide substrate
The local cryo-EM map of CATSPEREpsilon of Monomer A of the CatSper dimer
The local cryo-EM map of CATSPEREpsilon of Monomer B of the CatSper dimer
The local cryo-EM map of the gamma-gamma interface of the CatSper trimer
The local cryo-EM map of CATSPERBeta of Monomer A of the CatSper dimer
The local cryo-EM map of CATSPERGamma of Monomer B of the CatSper dimer
The local cryo-EM map of the extracellular region of the Monomers B and A' of the CatSper trimer