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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;
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- 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
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Recent Entries
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Cryo-EM map of respirasome open state 1 in presence of metformin (SC-MetO1), complex I proximal membrane arm focused
Cryo-EM map of respirasome open state bound by proguanil (SC-ProgO), complex I peripheral arm focused
Cryo-EM map of respirasome open state 1 in presence of metformin (SC-MetO1), complex III2 focused
Cryo-EM map of respirasome open state bound by proguanil (SC-ProgO)
Cryo-EM structure of the ICT01-BTN3A1/BTN3A2 complex, local refinement
Cryo-EM structure of the ICT01-BTN2A1/BTN3A1/BTN3A2 complex, local refinement
Cryo-EM structure of the ICT01-BTN2A1/BTN3A1/BTN3A2 complex (2 fabs)
Cryo-EM structure of the SPS3-FBN5 complex in a 2:2 state (class 3)
Cryo-EM structure of amyloid peptide-silk block protein fibril, Type 1
Cryo-EM structure of amyloid peptide-silk block protein fibril, Type 3
Complex I form respirasome open state bound by proguanil (SC-ProgO)
Cryo-EM structure of E.coli transcription initiation complex with Escherichia phage Mu late transcription activator C
Cryo-EM structure of E.coli transcription initiation complex with Escherichia phage Mu middle transcription activator Mor
Cryo-EM structure of the SPS3-FBN5 complex from Oryza sativa in complex with cobalt and geranylgeranyl S-thiodiphosphate (GGSPP)
Group II intron assembly intermediate Domain 1, 2, 3 and 4 "Fully open" state
Respiratory supercomplex CI2-CIII2-CIV2 (megacomplex, C1 symmetry) from alphaproteobacterium
Sub-tomogram average of the wild-type C. elegans I1III2 respiratory supercomplex
Influenza Neuraminidase in complex with N-Acyl Oseltamivir inhibitor
Influenza Neuraminidase in complex with N-Acyl Oseltamivir inhibitor
Influenza Neuraminidase in complex with N-Acyl Oseltamivir inhibitor
Soft-landed and rehydrated beta-galactosidase (averaged structure)
Translational activators Aep1, Aep2 and Atp25 in complex with mRNA and the yeast mitochondrial ribosome (consensus)
Sub-tomogram average of the wild-type C. elegans ATP synthase dimer (narrow membrane curvature)
Sub-tomogram average of nduf-11(RNAi) C. elegans respiratory complex I
Sub-tomogram average of the nduf-11(RNAi) C. elegans ATP synthase dimer (intermediate membrane curvature)
Sub-tomogram average of the wild-type C. elegans ATP synthase dimer (intermediate membrane curvature)
Sub-tomogram average of the wild-type C. elegans ATP synthase dimer (wide membrane curvature)
Sub-tomogram average of the nduf-11(RNAi) C. elegans ATP synthase dimer (wide membrane curvature)
Sub-tomogram average of the nduf-11(RNAi) C. elegans ATP synthase dimer (narrow membrane curvature)
Cryo-EM Structure of the Vaccinia Virus Entry/Fusion Complex (EFC) Lacking the F9 Subunit
Cryo-EM structure of soluble methane monooxygenase hydroxylase from Methylosinus sporium 5
Cryo-EM Structure of the Vaccinia Virus Entry/Fusion Complex (EFC) Including the F9 Subunit
Cryo-EM structure of human lipid phosphate phosphatase 1 complexed with LPA
Cryo-EM structure of the light-driven sodium pump ErNaR in the pentameric form
Cryo-EM structure of the light-driven sodium pump ErNaR in the monomeric form in the O2 state
Translational activators Aep1, Aep2 and Atp25 in complex with mRNA and the yeast mitochondrial ribosome (focused on the LSU)
Translational activators Aep1, Aep2 and Atp25 in complex with mRNA and the yeast mitochondrial ribosome (focused on the SSU head)
Translational activator Aep3 in complex with mRNA and the yeast mitochondrial ribosome (consensus map)
Translational activators Aep1, Aep2 and Atp25 in complex with mRNA and the yeast mitochondrial ribosome (focused on Aep1-Aep2-Atp25)
Translational activator Aep3 in complex with mRNA and the yeast mitochondrial ribosome (focused on Aep3)
Translational activators Aep1, Aep2 and Atp25 in complex with mRNA and the yeast mitochondrial ribosome (focused on the SSU body)
Translational activator Aep3 in complex with mRNA and the yeast mitochondrial ribosome (focused on the SSU)
Translational activator Aep3 in complex with mRNA and the yeast mitochondrial ribosome (focused on the SSU head)
Translational activator Aep3 in complex with mRNA and the yeast mitochondrial ribosome (focused on the LSU)
Translational activator Aep3 in complex with mRNA and the yeast mitochondrial ribosome
Translational activators Aep1, Aep2 and Atp25 in complex with mRNA and the yeast mitochondrial ribosome
High resolution structure of the thermophilic 60S ribosomal subunit of Chaetomium thermophilum
Connexin-32 (Cx32) gap junction channel in POPC-containing nanodiscs in the absence of CHS
Connexin-32 (Cx32) W3S mutant gap junction channel in POPC-containing MSP2N2 nanodiscs
Cryo-EM structure of the light-driven sodium pump ErNaR in the monomeric form in the K2 state
Deconvolved piDPC tomogram of lift-out lamellae from cell-derived matrices recorded on the Opal detector
Deconvolved piDPC tomogram of lift-out lamellae from cell-derived matrices
Deconvolved piDPC tomogram of lift-out lamellae from cell-derived matrices
Cryo-EM structure of E.coli transcription initiation complex with Escherichia phage Mu late transcription activator C focusing on C region
Cryo-EM structure of E.coli transcription initiation complex with Escherichia phage Mu late transcription activator C focusing on RNA polymerase region
Cryo-EM structure of E.coli transcription initiation complex with Escherichia phage Mu middle transcription activator Mor focusing on RNA polymerase region
Cryo-EM structure of E.coli transcription initiation complex with Escherichia phage Mu middle transcription activator Mor focusing on Mor region
Motor domain with ADP AAA1 and ADP AAA3 from yeast full-length dynein-1 in 0.1 mM ATP condition
Motor domain with Apo AAA1 and ADP AAA3 from yeast full-length dynein-1 in 0.1 mM ATP condition
Motor domain alone with Apo AAA1 and ADP AAA3 from yeast full-length dynein-1 and Pac1 in 0.1 mM ATP condition
Cryo-EM structure of rabbit TRPM3 in apo resting state at 37 degrees Celsius
Motor domain-Pac1 complex with ADP AAA1 and Apo AAA3 from yeast full-length dynein-1 and Pac1 in 0.1 mM ATP condition
Cryo-EM structure of rabbit TRPM3 in apo activated state at 18 degrees Celsius
Cryo-EM structure of rabbit TRPM3 in apo activated state at 37 degrees Celsius
Cryo-EM structure of rabbit TRPM3 in complex with CIM0216 in resting state at 18 degrees Celsius
Cryo-EM structure of rabbit TRPM3 in complex with primidone in resting state at 18 degrees Celsius
Cryo-EM structure of rabbit TRPM3 in complex with CIM0216 in activated state at 18 degrees Celsius
Cryo-EM structure of rabbit TRPM3 in complex with primidone in activated state at 18 degrees Celsius
Cryo-EM structure of rabbit TRPM3 in complex with CIM0216 at 18 degrees Celsius
Cryo-EM structure of apo rabbit TRPM3 having 2 resting and 2 activated subunits (ortho position) at 18 degrees Celsius
Cryo-EM structure of apo rabbit TRPM3 having 2 resting and 2 activated subunits (para position) at 18 degrees Celsius
Cryo-EM structure of apo rabbit TRPM3 having 1 resting and 3 activated subunits at 18 degrees Celsius
Cryo-EM structure of apo rabbit TRPM3 having 3 resting and 1 activated subunits at 18 degrees Celsius
Cryo-EM structure of apo rabbit TRPM3 having 2 resting and 2 activated subunits (para position) at 37 degrees Celsius
Cryo-EM structure of apo rabbit TRPM3 having 2 resting and 2 activated subunits (ortho position) at 37 degrees Celsius
Cryo-EM structure of apo rabbit TRPM3 having 3 resting and 1 activated subunits at 37 degrees Celsius
Cryo-EM structure of CIM0216-bound rabbit TRPM3 having 3 resting and 1 activated subunits at 18 degrees Celsius
Cryo-EM structure of apo rabbit TRPM3 having 1 resting and 3 activated subunits at 37 degrees Celsius
Cryo-EM structure of primidone-bound rabbit TRPM3 having 3 resting and 1 activated subunits at 18 degrees Celsius
Cryo-EM structure of CIM0216-bound rabbit TRPM3 having 2 resting and 2 activated subunits (ortho position) at 18 degrees Celsius
Cryo-EM structure of CIM0216-bound rabbit TRPM3 having 2 resting and 2 activated subunits (para position) at 18 degrees Celsius
Cryo-EM structure of CIM0216-bound rabbit TRPM3 having 1 resting and 3 activated subunits at 18 degrees Celsius
Cryo-EM structure of primidone-bound rabbit TRPM3 having 1 resting and 3 activated subunits at 18 degrees Celsius
Cryo-EM structure of primidone-bound rabbit TRPM3 having 2 resting and 2 activated subunits (para position) at 18 degrees Celsius
Helical assembly of the IL-17RA/RB/ACT1 complex upper part focused map
Helical assembly of the IL-17RA/RB/ACT1 complex lower part focused map
Masked Classification of Prohibitin Complexes Showing the Prohibitin complex with an Additional Matrix-Facing Density (Class 1)
Masked Classification of Prohibitin Complexes Showing the Prohibitin complex without an Additional Matrix-Facing Density (Class 2)
Human quaternary complex of a translating 80S ribosome, NAC, MetAP1 and NatD
S. thermophilus class III ribonucleotide reductase focused refined core
S. thermophilus class III ribonucleotide reductase with dATP and TTP
S. thermophilus class III ribonucleotide reductase with ATP and TTP
S. thermophilus class III ribonucleotide reductase signal subtracted cone domains and core
S. thermophilus class III ribonucleotide reductase signal subtracted cone domains and core
S. thermophilus class III ribonucleotide reductase focused refined core
Cryo-EM structure of the glycosyltransferase GtrB in the substrate-bound state
Cryo-EM structure of the glycosyltransferase GtrB in the pre-catalysis and product-bound state
Cryo-EM structure of the glycosyltransferase GtrB (tetramer volume)
Cryo-EM structure of the glycosyltransferase GtrB in the apo state (octamer volume)
Cryo-EM structure of the glycosyltransferase GtrB in the pre-intermediate state
Tomogram of bacteriophage NF5-infected Brochothrix thermosphacta cell (1 out of 2)
Tomogram of bacteriophage NF5-infected Brochothrix thermosphacta cell (2 out of 2)
Cryo-EM map of apo-XPF-ERCC1-SLX4(330-555)-SLX4IP from a DNA-containing sample.
Cryo-EM structure of a DNA-bound XPF-ERCC1-SLX4(330-555)-SLX4IP complex
In-situ structure of the flagellar motor of Campylobacter jejuni pflA deletion mutant
In-situ structure of the flagellar motor of Campylobacter jejuni rpoN deletion mutant
In-situ structure of the flagellar motor of Campylobacter jejuni pflC deletion mutant
In-situ structure of the flagellar motor of Campylobacter jejuni pflB deletion mutant
Cryo-EM structure of human sortilin ectodomain in complex with a thyroglobulin C-terminal peptide
Focused refinement map of in situ E-ring structure in Campylobacter jejuni flagellar motor
In-situ structure of the flagellar motor of Campylobacter jejuni flgY deletion mutant
In-situ structure of the flagellar motor of Campylobacter jejuni fcpMNO deletion mutant
Half of Campylobacter jejuni motA deletion mutant flagellar motor structure in situ
Focused refinement map of in situ spoke-rim structure in Campylobacter jejuni flagellar motor
Half of Campylobacter jejuni pflD deletion mutant flagellar motor structure in situ
In-situ structure of the flagellar motor of Campylobacter jejuni pflD deletion mutant
Half of Campylobacter jejuni fcpMNO deletion mutant flagellar motor structure in situ
beta-barrel assembly machine from Escherichia coli in an early state of substrate assembly
Focused refinement of the barrel region of beta-barrel assembly machine from Escherichia coli in an late state of substrate assembly
beta-barrel assembly machine from Escherichia coli in a late state of substrate assembly
beta-barrel assembly machine from Escherichia coli in a middle state of substrate assembly
Consensus refinement of the barrel region of beta-barrel assembly machine from Escherichia coli in an late state of substrate assembly
Native GluN1/GluN2A/GluNx in complex with 5F11 and 3D2 Fabs (class 2), glycine and glutamate-bound state
Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with bound plastocyanin
GluN1/GluN2A in complex with 3D2 Fab, glycine and glutamate-bound state
Native GluN1/GluNx in complex with 5F11 Fab (class 5), glycine and glutamate-bound state
Native GluN1/GluN2A/GluN2B in complex with 5F11 and 3D2 Fabs (class 1), glycine and glutamate bound state
GluN1/GluN2A in complex with polyclonal autoantibody Fab fragments (class 1), glycine- and glutamate-bound state
Native GluN1/GluN2A in complex with 5F11 and 3D2 Fabs, local ATD dimer
GluN1/GluN2A in complex with polyclonal autoantibody Fab fragments (class 2), glycine- and glutamate-bound state
Native GluN1/GluN2B in complex with 5F11 Fab (class 4), glycine and glutamate-bound state
Native GluN1/GluN2A in complex with 5F11 and 3D2 Fabs (class 3), glycine and glutamate-bound state
Sampling-mismatch-uncorrected ptychographic SPA reconstruction of the Thermoplasma acidophilum 20S proteasome
Sampling-mismatch-corrected ptychographic SPA reconstruction of the Thermoplasma acidophilum 20S proteasome
Single-particle cryo-EM structure of the first variant of mobilized colistin resistance (MCR-1) in its ligand-bound state
Rabbit muscle aldolase cryo-EM reconstruction obtained from Krios 5 with Selectris-X Falcon 4i detector
Cryo-EM structure of J601-1B2 Fab in complex with HIV-1 BG505 DS-SOSIP Env trimer
Cryo-EM structure of K001-A1 Fab in complex with HIV-1 459C-OPT RnS DS-SOSIP Env trimer
Cryo-EM structure of J601-A6 Fab in complex with HIV-1 BG505 DS-SOSIP Env trimer
Cryo-EM structure of Vibrio cholerae RNA polymerase holoenzyme bound to an ompU promoter DNA fragment
Focused map #2 of the cryo-EM structure of Vibrio cholerae RNA polymerase Transcription Activation Complex with ToxR and TcpP transcription factors and bound to a toxT promoter DNA fragment
Cryo-EM structure of Vibrio cholerae RNA polymerase Transcription Activation Complex with TcpP transcription factor and a toxT promoter DNA fragment
Focused map #1 of the cryo-EM structure of Vibrio cholerae RNA polymerase Transcription Activation Complex with ToxR and TcpP transcription factors and bound to a toxT promoter DNA fragment
Consensus map of the cryo-EM structure of Vibrio cholerae RNA polymerase Transcription Activation Complex with ToxR transcription factor and bound to an ompU promoter DNA fragment
Cryo-EM structure of Vibrio cholerae RNA polymerase holoenzyme bound to an ompU promoter DNA fragment and 5-mer RNA
Consensus map of the cryo-EM structure of Vibrio cholerae RNA polymerase Transcription Activation Complex with TcpP transcription factor and bound to a toxT promoter DNA fragment
Focused map #1 of the cryo-EM structure of Vibrio cholerae RNA polymerase Transcription Activation Complex with TcpP transcription factor and bound to a toxT promoter DNA fragment
Cryo-EM structure of Vibrio cholerae RNA polymerase Transcription Activation Complex with ToxR and TcpP transcription factors and a toxT promoter DNA fragment
Cryo-EM structure of Vibrio cholerae RNA polymerase dimer with ToxR and TcpP transcription factors and a toxT promoter DNA fragment
Focused map #1 of the cryo-EM structure of Vibrio cholerae RNA polymerase Transcription Activation Complex with ToxR transcription factor and bound to an ompU promoter DNA fragment
Focused map #2 of the cryo-EM structure of Vibrio cholerae RNA polymerase Transcription Activation Complex with TcpP transcription factor and bound to a toxT promoter DNA fragment
Focused map #2 of the cryo-EM structure of Vibrio cholerae RNA polymerase Transcription Activation Complex with ToxR transcription factor and bound to an ompU promoter DNA fragment
Cryo-EM structure of Vibrio cholerae RNA polymerase Transcription Activation Complex with ToxR transcription factor and ompU promoter DNA
Consensus map of the cryo-EM structure of Vibrio cholerae RNA polymerase Transcription Activation Complex with ToxR and TcpP transcription factors and bound to a toxT promoter DNA fragment
Cryo-EM map of respirasome open state bound by proguanil (SC-ProgO), complex I distal membrane arm focused
Cryo-EM map of respirasome open state 1 in presence of metformin (SC-MetO1), complex I distal membrane arm focused
Cryo-EM map of respirasome open state 1 in presence of metformin (SC-MetO1)
Cryo-EM map of respirasome open state bound by proguanil (SC-ProgO), complex I proximal membrane arm focused
Cryo-EM map of respirasome open state 1 in presence of metformin (SC-MetO1), complex IV focused
Cryo-EM map of respirasome open state 1 in presence of metformin (SC-MetO1), complex I peripheral arm focused