About EMDB
Meet the team
The Electron Microscopy Data Bank (EMDB) team operates out of EMBL-EBI and you can read more about us here.
EMDB history
The 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.
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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.
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Recent Entries
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Structure of the 70S ribosome with E- and P-site tRNA from the alphaproteobacteria Asaia platycodi.
Map of the 70S ribosome with E-site tRNA and HPF from the alphaproteobacteria Rhodospirillum rubrum.
Map of the 70S ribosome with E- and P-site tRNA from the gammaproteobacteria Escherichia coli.
Map of the 70S ribosome with E-site tRNA and HPF from the gammaproteobacteria Escherichia coli.
Map of the 70S ribosome with E- and P-site tRNA from the alphaproteobacteria Rhodospirillum rubrum.
Two Component Protein Nano-Particle (T=3). De Novo Design, Computationally Relaxed into Low Resolution Subtomogram Averaged CryoEM Map with Icosahedral Symmetry Applied
Structure of a stalled E. coli 70S RNC-NuoK-48 in complex with the SecYEG Translocon.
Structure of a stalled E. coli 70S RNC-NuoK-48 in complex with the SecYEG Translocon (Focused Refinement)
Structure of a stalled E. coli 70S RNC-NuoK-86 in complex with the SecYEG-YidC membrane protein insertase (Focused Refinement)
Structure of a stalled E. coli 70S RNC-NuoK-86 in complex with the SecYEG-YidC membrane protein insertase
Structure of a stalled E. coli 70S RNC-NuoK-86-E36K-E76K-mutant in complex with the SecYEG-YidC membrane protein insertase (Focused Refinement)
Structure of a stalled E. coli 70S RNC-NuoK-86-E36K-E76K-mutant in complex with the SecYEG-YidC membrane protein insertase
Focused map of LRRC58-CDO1 region from LRRC58- EloB/C-CDO1 in complex with neddylated CUL2-RBX1-ARIH1-Ub
Focused map of ARIH1-Ub region from LRRC58- EloB/C-CDO1 in complex with neddylated CUL2-RBX1-ARIH1-Ub
Focused map of LRRC58-CDO1 region from LRRC58-ELOB/C-CDO1-CUL5-RBX2-NEDD8-ARIH2-UB
Consensus Map of LRRC58-ELOB/C-CDO1 in complex with NEDD8-CUL5-RBX2-ARIH2-Ub
Structure of the human inner kinetochore CCAN bound to a mono-CENP-A nucleosome
Consensus map of LRRC58- EloB/C-CDO1 in complex with neddylated CUL2-RBX1-ARIH1-Ub
Structure of the human inner kinetochore CCAN bound to a 3' CENP-A nucleosome
Structure of the human inner kinetochore CCAN bound to a 5' CENP-A nucleosome
Focused map of CUL2-LRRC58-EloC interface region from LRRC58- EloB/C-CDO1 in complex with neddylated CUL2-RBX1-ARIH1-Ub
Structure of LRRC58-EloB/C-CDO1 in complex with NEDD8-CUL5-RBX2-ARIH2-Ub
1.80 A cryo-EM structure of Mycobacterium tuberculosis BfrB prepared under isotope-depleted abundance
Structure of the human inner kinetochore CCAN bound to a di-CENP-A nucleosome
1.79 A cryo-EM structure of Mycobacterium tuberculosis BfrB prepared under natural isotope abundance
Structure of the human inner kinetochore CCAN bound to a di-CENP-A nucleosome, consensus map
Structure of the human inner kinetochore CCAN and CENP-C bound to DNA
CryoEM structure of native quinol dependent Nitric Oxide Reductase with HQN at pH 6.5
CryoEM structure of native quinol dependent Nitric Oxide Reductase at pH 8.0.
CryoEM structure of quinol dependent Nitric Oxide Reductase with BRIL
Cryo-EM structure of DddT G101D in substrate-free outward open conformation
Cryo-EM structure of DddT G101D in substrate-free inward open conformation
Cryo-EM structure of human Nav1.6 in complex with Iota-Conotoxin RXIA
Cryo-EM structure of DddT in closed substrate-free conformation in the presence of potassium ions and dimethylsulfoniopropionate
Cryo-EM structure of human Nav1.6 in complex with delta-paraponeritoxin-Pc1a
Electron tomogram of resin-embedded yeast cells expressing Tcb3(1-272)-GFP-chimeraC, deleted for tcb1/2, scs2/22 and ist2
Structure of human MCM2-7 single hexamer without MCM3 CTE, state 2
Structure of human MCM2-7 single hexamer without MCM3 CTE, state 1
CryoEM structure of Arabidopsis thaliana Col-0 Rubisco with D4 symmetry
Structure of human MCM2-7 single hexamer with MCM3-WHD attached to MCM2-CTD
Structure of human MCM2-7 single hexamer with MCM3-WHD attached to MCM2-CTD, state 2
Structure of human MCM2-7 single hexamer with MCM3-WHD attached to MCM2-CTD, state 3
Structure of human MCM2-7 single hexamer with MCM3-WHD attached to MCM2-CTD, containing Meier-Gorlin Syndrome mutation (MCM3-Q761L)
CryoEM structure of Arabidopsis thaliana M309I Rubisco with D4 symmetry
CryoEM structure of Arabidopsis thaliana D397N Rubisco with D4 symmetry
Composite map of LRRC58- EloB/C-CDO1 in complex with neddylated CUL2-RBX1-ARIH1-Ub
Asymmetric reconstruction of immature TBEV particle with 2 missing pentamers
Asymmetric reconstruction of immature TBEV particle with 2 irregularities
Cryo-EM structure of Beta-lactamase-like domain from Neomoorella carbonis
Immature TBEV envelope spike with interaction partners underneath - SPA
Asymmetric reconstruction of immature TBEV particle with altered 5-fold
Immature TBEV envelope spike with interaction partners underneath - STA
Phage 812 baseplate in the pre-contraction state - upper arm (segment B)
Phage 812 baseplate in the pre-contraction state - core and wedge module proteins
Phage 812 baseplate in the pre-contraction state - lower arm (segment C)
Phage 812 baseplate in the pre-contraction state - lower arm (lRBP1-uRBP2)
Phage 812 baseplate in the pre-contraction state - lower arm (uRBP1-lRBP2)
Phage 812 baseplate in the pre-contraction state - lower arm (segment DEF)
Phage 812 baseplate in the pre-contraction state - upper arm (segment CDEF)
Phage 812 baseplate in the pre-contraction state - lower arm (segment B)
Phage 812 baseplate in the pre-contraction state - upper arm (segment A)
Phage 812 baseplate in the pre-contraction state - tail sheath initiator and baseplate-proximal tail proteins
Phage 812 baseplate in the pre-contraction state - lower arm (segment A)
Baseplate arm (segment B) of phage 812 in the post-contraction state
E. coli 70S ribosome, trapped conformational excited state of SSU-h44 apical loop, with A/P- and P/E-site tRNA
E. coli 70S ribosome, trapped conformational excited state of SSU-h44 apical loop, with A- and P-site tRNA
E. coli 70S ribosome, trapped conformational ground state of SSU-h44 apical loop, with A- and P-site tRNA
E. coli 70S ribosome, trapped conformational ground state of SSU-h44 apical loop, with A/P- and P/E-site tRNA
E. coli 70S ribosome, conformational ground state mutation in SSU-h41, with A/P- and P/E-site tRNA
E. coli 70S ribosome, conformational ground state mutation in SSU-h41, with A- and P-site tRNA
E. coli 70S ribosome, trapped conformational ground state of SSU-h44 apical loop, with P-site tRNA
E. coli 70S ribosome, conformational excited state mutation in SSU-h41, with A- and P-site tRNA
E. coli 70S ribosome, conformational excited state mutation in SSU-h41, with A/P- and P/E-site tRNA
E. coli 70S ribosome, trapped conformational ground state of SSU-h44 apical loop, with A- and P/E-site tRNA
E. coli 70S ribosome, trapped conformational ground state of SSU-h44 apical loop, without tRNA
E. coli 70S ribosome, trapped conformational ground state of SSU-h44 apical loop, with P/E-site tRNA
E. coli 70S ribosome, trapped conformational excited state of SSU-h44 apical loop, with P-site tRNA
E. coli 70S ribosome, trapped conformational excited state of SSU-h44 apical loop, without tRNA
E. coli 70S ribosome, trapped conformational excited state of SSU-h44 apical loop, with A- and P/E-site tRNA
E. coli 70S ribosome, trapped conformational excited state of SSU-h44 apical loop, with P/E-site tRNA
E. coli 70S ribosome, conformational ground state mutation in SSU-h41, with A- and P/E-site tRNA
E. coli 70S ribosome, conformational ground state mutation in SSU-h41, without tRNA
E. coli 70S ribosome, conformational excited state mutation in SSU-h41, with A- and P/E-site tRNA
E. coli 70S ribosome, conformational ground state mutation in SSU-h41, with P-site tRNA
E. coli 70S ribosome, conformational excited state mutation in SSU-h41, without tRNA
E. coli 70S ribosome, conformational ground state mutation in SSU-h41, with P/E-site tRNA
E. coli 70S ribosome, conformational excited state mutation in SSU-h41, with P-site tRNA
E. coli 70S ribosome, conformational excited state mutation in SSU-h41, with P/E-site tRNA
Cryo-EM structure of alpha-synuclein filaments from Parkinson's disease with G51D mutaion in SNCA
Cryo-EM structure of alpha-synuclein filaments from Parkinson's disease with H50Q variant in SNCA
N. brasiliensis GlfT2 in a styrene maleic acid liponanoparticle (C1 Unmasked Map)
Structure of Rapidly twisting Amyloid-beta 40 fibril , RT-Ab40(C1)'
Ternary complex structure of compound 1 bound to SMARCA2 bromodomain and DCAF16:DDB1deltaBPB
Cryo-EM structure of the Class 3 PI3K alpha/KRas complex on POPC/POPS nanodiscs
Cryo-EM structure of the PI3K alpha/KRas complex on POPC/POPS/PIP2 nanodiscs low-pass filtered to 5 angstroms
Cryo-EM structure of active mutant human green cone opsin (E129Q) in complex with chimeric G protein (miniGist)
Structure of Rapidly twisting Amyloid-beta 40 fibril , RT-Ab40(C2)
Structure of Rapidly twisting Amyloid-beta 40 fibril , RT-Ab40(C1)
Local refinement of active human green opsin mutant E129Q in complex with chimeric G protein
Structure of Rapidly twisting Amyloid-beta 40 fibril , RT-Ab40(2_1)
Single particle reconstruction of PilU from Vibrio cholerae El Tor E7946, form 2
Single particle reconstruction of PilU from Vibrio cholerae El Tor E7946, form 4
Single particle reconstruction of PilU from Vibrio cholerae El Tor E7946, form 3
Single particle reconstruction of PilU from Vibrio cholerae El Tor E7946, form 1
Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B
Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES) and hygromycin B, Class II
Structure of Geobacillus stearothermophilus RNase P ribozyme sub-conformation 3
Structure of Geobacillus stearothermophilus RNase P ribozyme in 5 mM Mg2+
Structure of Geobacillus stearothermophilus RNase P ribozyme sub-conformation 1
Structure of Geobacillus stearothermophilus RNase P ribozyme in complex with precursor tRNA in 5 mM Ca2+
Structure of Geobacillus stearothermophilus RNase P ribozyme in complex with mature tRNA in 5 mM Ca2+
Structure of Geobacillus stearothermophilus RNase P ribozyme tetraloop mutant (sub-conformation 2)
Structure of Geobacillus stearothermophilus RNase P ribozyme in 10 mM Mg2+
Structure of Geobacillus stearothermophilus RNase P ribozyme tetraloop mutant (sub-conformation 1)
Structure of Geobacillus stearothermophilus RNase P ribozyme in complex with mature tRNA in 10 mM Ca2+
Structure of Geobacillus stearothermophilus RNase P ribozyme sub-conformation 2
Cryo-EM structure of the PGD2-bound prostaglandin D2 receptor (DP1)-Gs complex (G protein-focused map)
Cryo-EM structure of the BW245C-bound prostaglandin D2 receptor (DP1)-Gs complex (Receptor-focused map)
Cryo-EM structure of the PGD2-bound prostaglandin D2 receptor (DP1)-Gs complex (Consensus map)
Cryo-EM structure of the BW245C-bound prostaglandin D2 receptor (DP1)-Gs complex (Consensus map)
Structure of Geobacillus stearothermophilus RNase P ribozyme tetraloop mutant (sub-conformation 3)
Cryo-EM structure of the PGD2-bound prostaglandin D2 receptor (DP1)-Gs complex (Receptor-focused map)
Cryo-EM structure of Pseudomonas aeruginosa outer-membrane lipoprotein PA3214 in the open conformation
Two Component Protein Nano-Particle (T=3). De Novo Design, Computationally Relaxed into Low Resolution Single Particle CryoEM Map with Icosahedral Symmetry Applied
Cryo-EM structure of the BW245C-bound prostaglandin D2 receptor (DP1)-Gs complex (G protein-focused map)
Cryo-EM structure of Pseudomonas aeruginosa soluble lipoprotein PA3214
Cryo-EM structure of Pseudomonas aeruginosa outer-membrane lipoprotein PA3214 bound to MCE protein PA3213 C-terminal peptide (CASP target)
Locally refined DeepEMhanced map of the meizothrombinDESF1-factor Xa complex
Composite map of the meizothrombinDESF1, factor Xa and factor Va complex
Locally refined DeepEMhanced map of the factor Xa-factor Va complex
RNA Vault Shoulder with ADPR bound, compact conformation, focused refinement (MVP/PARP4/TEP1 NADP sample)
Composite map of hypomethylated 80S ribosome treated with hygromycin B
RNA Vault bound to PARP4 MINT, focused refinement (MVP/PARP4/TEP1 NADP sample)
Human Brain RNA Vault Shoulder bound to ADPR, focused refinement (EMPIAR-10766)
Consensus map of the meizothrombinDESF1, factor Xa, factor Va complex
RNA Vault shoulder region with BAD bound, focused refinement (MVP/TEP1 sample)
RNA Vault Shoulder with ADPR bound, extended conformation, focused refinement (MVP/PARP4/TEP1 NADP sample)