About EMDB
The Electron Microscopy Data Bank (EMDB) is a public repository for cryogenic-sample Electron Microscopy (cryoEM) volumes and representative tomograms of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, helical reconstruction, electron tomography, subtomogram averaging, and electron crystallography (for more information, see the EMDB Policies).
EMDB was founded at EMBL-EBI in 2002 under the leadership of Kim Henrick. From 2007, the archive has been operated jointly by EMBL-EBI and the Research Collaboratory for Structural Bioinformatics (RCSB)a. In 2013, the Protein Data Bank Japan (PDBj) also became involved in EMDB. As of the first of January, 2021, EMDB is an archive operated under the aegis of the Worldwide Protein Data Bank (wwPDB), and has also joined that organisation as a full member.
Results of cryo-EM studies are archived in three collaborating archives:
- EMDB stores the processed 3D volumes and tomograms;
- PDB stores any atomic models that have been constructed based on EMDB data;
- EMPIAR stores the raw EM data underpinning the data in EMDB/PDB.
Data for EMDB and PDB can be deposited through the wwPDB deposition and annotation system OneDep.
EMPIAR (Electron Microscopy Public Image Archive) is a companion archive to EMDB, founded at and operated by EMBL-EBI, and with a mirror site at PDBj.
Citing EMDB
Please cite the following publication in your papers and on websites: The wwPDB Consortium, EMDB—the Electron Microscopy Data Bank, Nucleic Acids Research, Volume 52, Issue D1, 5 January 2024, Pages D456–D465, https://doi.org/10.1093/nar/gkad1019
To cite individual entries, please quote the EMDB accession code(s) and cite the original publication(s) in which the entries are described.
EMDB logos and branding should not be used on public-facing websites unless explicit prior permission has been obtained from us. However, if you want to use an EMDB logo in a presentation or report, you can use the images in the following table royalty-free and without the need to obtain prior permission from us.
More information
Please see our FAQ, Policies, description of the EMDB data model, or contact the EMDB helpdesk.
Funding
The work on EMDB at EMBL-EBI has been funded in the past by the European Commission, NIH, UKRI-BBSRC and EMBL-EBI (through the EMBL member states). It is currently funded by the Wellcome Trust and EMBL-EBI.
Quick links
Recent Entries
(Show all)Trimeric prM/E spike of Tick-borne encephalitis virus immature particle
Cryo-electron tomogram of small unilamellar vesicles decorated with poliovirus protein 2C
Archaellum filament from the Halobacterium salinarum deltaAgl27 strain
Cryo EM map of the type 2A polymorph of alpha-synuclein at pH 7.0.
Tick-borne encephalitis virus (strain Neudoerfl) immature particle
Archaellum filament from the Halobacterium salinarum deltaAgl26 strain
Structure of human terminal uridylyltransferase 4 (TUT4, ZCCHC11) in complex with pre-let7g miRNA and Lin28A
Subtomogram average of 80S ribosomes in S. cerevisiae under acute glucose starvation
Cryo EM structure of the type 3B polymorph of alpha-synuclein at low pH.
DIV 1 hippocampal neuron (weighted back-projection and greyscale segmentation)
MicroED structure of SARS-CoV-2 main protease (MPro/3CLPro) with missing cone eliminated by suspended drop
ApoRF3 bound to an E. coli non-rotated ribosome termination complex, from focused classification and refinement (State I-B)
Cryo-EM structure of an E. coli non-rotated ribosome termination complex bound with RF1, P- and E-site tRNAPhe (State I-A)
RF3-GDPCP bound to an E. coli rotated ribosome, from focused classification and refinement (State II-C)
Cryo-EM structure of an E. coli non-rotated ribosome termination complex bound with RF1, P- and E-site tRNAPhe (State II-D)
Cryo-EM structure of an E. coli non-rotated ribosome termination complex bound with apoRF3, RF1, P- and E-site tRNAPhe (State I-B)
Cryo-EM structure of an E. coli non-rotated ribosome termination complex bound with RF3-GDPCP, RF1, P- and E-site tRNAPhe (Composite state II-A)
Cryo-EM structure of an E. coli non-rotated ribosome termination complex bound with RF3-GDPCP, RF1, P- and E-site tRNAPhe (State II-A)
Cryo-EM structure of an E. coli rotated ribosome bound with RF3-GDPCP and p/E-tRNAPhe (Composite state II-C)
Phosphorylated, ATP-bound, E1371Q human cystic fibrosis transmembrane conductance regulator (E1371Q-CFTR)
Cryo-EM structure of alpha5beta1 integrin in complex with NeoNectin
RF3-GDPCP bound to an E. coli rotated ribosome, from focused classification and refinement (State II-B)
Cryo-EM structure of an E. coli non-rotated ribosome termination complex bound with apoRF3, RF1, P- and E-site tRNAPhe (Composite state I-B)
Cryo-EM structure of an E. coli rotated ribosome bound with RF3-GDPCP and p/E-tRNAPhe (State II-C)
Cryo-EM structure of an E. coli rotated ribosome bound with RF3-GDPCP and p/E-tRNAPhe (Composite state II-B)
Complex of NPR1 ectodomain and REGN5381 Fab in an active-like state with no ANP bound
Cryo-EM structure of an E. coli rotated ribosome bound with RF3-GDPCP and p/E-tRNAPhe (State II-B)
Phosphorylated, ATP-bound, inhibitor 172-bound E1371Q human cystic fibrosis transmembrane conductance regulator
RF3-GDPCP bound to an E. coli non-rotated ribosome termination complex, from focused classification and refinement (State II-A)
Complex of NPR1 ectodomain with ANP plus an allosteric activating antibody, REGN5381
Structure of HCoV-HKU1C spike in the functionally anchored-1up conformation with 1TMPRSS2
Cryo-EM structure of human ABCC4 in complex with ANP-bound in NBD1 and METHOTREXATE
Structure of HCoV-HKU1C spike in the functionally anchored-3up conformation with 3TMPRSS2
Structure of HCoV-HKU1C spike in the functionally anchored-2up conformation with 2TMPRSS2
Structure of HCoV-HKU1A spike in the functionally anchored-3up conformation with 3TMPRSS2
Local structure of HCoV-HKU1C spike in complex with TMPRSS2 and glycan
Structure of HCoV-HKU1C spike in the functionally anchored-3up conformation with 2TMPRSS2
Local structure of HCoV-HKU1A spike in complex with TMPRSS2 and glycan
Structure of HCoV-HKU1C spike in the glycan-activated-closed conformation
Structure of HCoV-HKU1C spike in the glycan-activated-2up conformation
Structure of HCoV-HKU1C spike in the glycan-activated-1up conformation
Structure of HCoV-HKU1C spike in the glycan-activated-3up conformation
Structure of HCoV-HKU1C spike in the inactive-closed conformation
ICP1 Csy-dsDNA-Cas1-Cas2/3 complex (fully assembled form), C2 symmetry
CryoEM structure of the transketolase ANIP from Streptomyces hygrospinosus
ICP1 Csy-dsDNA-Cas1-Cas2/3 complex (fully assembled form) composited structure with C1 symmetry