Documentation
Summary
EMDB documentation pages are indexed below. These documents are intended to provide user focused guidance on systems and services that are provided by the EMDB or by our partners through our services, in particular our partners of the wwPDB.
Table of contents
- General
- Deposition (OneDep)
- EMDB Services
- Miscellaneous
Contact us
Getting in touch: if anything he needs clarification, please reach out to us at the EMDB helpdesk. Important: for any matters related to an active deposition, please only reach out to us through the OneDep deposition system in the communication module of your active deposition.
General
EMDB data model
Data models which describe entries in the database are maintained by the EMDB and the wwPDB. Users will find two data models in which metadata information on database entries can be found, XML and CIF. In practise, for supplying metadata directly to a deposition, users and software developers should use CIF.
→ View data model documentation
Policies
EMDB policies are developed to convey policies specific to our systems and services. Where the EMDB is a core member of the wwPDB consortium, our EMDB policies were developed to complement wwPDB policies. Our processes are governed by both policy documents and are under continuous review to harmonise them.
Deposition (OneDep)
General deposition
The EMDB maintains a general deposition guide. This document is complimentary to basic OneDep deposition information here. In cases of uncertainty please contact us.
→ Read general deposition guide
→ Open OneDep general deposition guide
Composite map deposition
Depositors can find a guide with specific guidance on how to approach the submission of composite maps and their constituent consensus and focus refinements. This guide aims to provide a strategy for completing this kind of deposition efficiently whilst aligning the entries with community derived policy on composite maps.
→ Read composite map deposition guide
EMDB Services
Search engine
Search of the EMDB is powered by Solr provided by EBI. This drives the search functionality of the website but also up-to-date entry page cross referencing. The system can be utilized to create queries that return archive wide metadata.
→ Explore search engine documentation
→ Check the list of available search fields
Chart builder
Built on top of EMDB search, specialized queries are made by the EMDB Chart Builder to plot archive wide metadata and derivative analyses in live interactive charts.
→ Learn how to use the Chart Builder
EMICSS
This system uses data provided at the point of deposition to systematically search associated databases for information which may be used to enrich the annotations of entries.
Validation Analysis
The validation pipeline developed by the EMDB for 3DEM data and associated model coordinates generates validation data for entries when they are deposited to the wwPDB via OneDep. These are the validation data that are communicated to manuscript peer reviewers via the wwPDB PDF validation report. Additional validation data are generated upon data release (normally upon manuscript publication) and communicated to the public via EMDB entry pages on the validation tab.
→ View validation analysis documentation
API
The EMDB Application Programming Interfaces (APIs) provide rapid, scalable and automatable access to 3DEM reconstruction metadata and data. The APIs currently are dedicated to serve (1) main archive, added-value (2) quality validation and (3) semantic annotation metadata and data. A python wrapper provides unified access to selected endpoints across all of the APIs.
Miscellaneous
Frequently Asked Questions (FAQ)
Answers to common questions about EMDB data, deposition, services, and policies.
→ Browse frequently asked questions
Selected Publications
- Fonseca, N., et al. (in press). Chart Builder: An Interactive Tool for User Driven Data Visualization in the Electron Microscopy Data Bank. Frontiers
- Pintilie, G., et al. (2025). Q-score as a reliability measure for protein, nucleic acid and small-molecule atomic coordinate models derived from 3DEM maps. Acta Cryst. D. doi.org/10.1107/S2059798325005923
- Duraisamy, A. K., et al. (2025). EMICSS: Added-value annotations for EMDB entries. Bioinformatics Advances. doi.org/10.1093/bioadv/vbaf203
- Kleywegt, G. J., et al. (2024). Community recommendations on cryoEM data archiving and validation. IUCrJ. doi.org/10.1107/S2052252524001246
- The wwPDB consortium., (2024). EMDB - the Electron Microscopy Data Bank. Nucleic Acids Research. doi.org/10.1093/nar/gkad1019
- Patwardhan, A., et al. (2017). Building bridges between cellular and molecular structural biology. eLife. doi.org/10.7554/eLife.25835
- Patwardhan, A., et al. (2014). A 3D cellular context for the macromolecular world. Nature Structural & Molecular biology. doi.org/10.1038/nsmb.2897
- Patwardhan, A., et al. (2012). Data management challenges in three-dimensional EM. Nature Structural & Molecular Biology. doi.org/10.1038/nsmb.2426
Under development
Segmentation data model prototype.
Quick links
Recent Entries
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Tomogram of mitochondria in T cell from older patients after restimulation
Cryo-EM structure of the ARISCdC(E33A):K63-Ub4 complex (Left Arm map)
Cryo-EM structure of the ARISC(E33A)-RAP80:K63-Ub7 complex (Ub (P2) and Ub (P3) map)
Cryo-EM structure of the ARISC(E33A)-RAP80:K63-Ub7 complex (Left Arm map)
EcMscM lacking the first periplasmic helical bundle and the cytoplasmic extension of TM7 in NaCl in a closed conformation
Rad55-Rad57-SHU-Rad51-Rad51 bound to ssDNA with AMP-PNP. Local map focused on Rad51
Rad55-Rad57-SHU-Rad51-Rad51 bound to ssDNA with AMP-PNP. Local map focused on SHU
Cryo-EM structure of single-bound FDG antibody VRC49.01 in complex with HIV-1 Env BG505 DS-SOSIP trimer
Cryo-EM structure of Broadly neutralizing antibody VRC48.02 in complex with HIV-1 Env BG505 DS-SOSIP trimer
Rad55-Rad57(E161Q)-SHU-Rad51-Rad51 bound to ssDNA with ATP. Local map focused on Rad55/Rad57
Rad55-Rad57-SHU-Rad51-Rad51 bound to ssDNA with AMP-PNP. Composite map
Core of EcMscM lacking the first periplasmic helical bundle in NaCl in a closed conformation
Rad55-Rad57-SHU-Rad51-Rad51 bound to ssDNA with AMP-PNP. Local map focused on Rad55/Rad57
Cryo-EM structure of triple-bound FDG antibody VRC49.01 in complex with HIV-1 Env BG505 DS-SOSIP trimer
EcMscM in KCl in an open conformation with density for the second periplasmic helical bundle
EcMscM lacking the first periplasmic helical bundle in KCl in an open conformation
EcMscM lacking the first periplasmic helical bundle in NaCl in a closed conformation
Core of EcMscM lacking the first periplasmic helical bundle and the cytoplasmic extension of TM7 in NaCl in a closed conformation
Cryo-EM structure of double-bound FDG antibody VRC49.01 in complex with HIV-1 Env BG505 DS-SOSIP trimer
Rad55-Rad57(E161Q)-SHU-Rad51-Rad51 bound to ssDNA with ATP. Composite map
Rad55-Rad57(E161Q)-SHU-Rad51-Rad51 bound to ssDNA with ATP. Local map focused on SHU
Rad55-Rad57(E161Q)-SHU-Rad51-Rad51 bound to ssDNA with ATP. Local map focused on Rad51
Rad55-Rad57(E161Q)-SHU-3xRad51 bound to ssDNA with ATP. Local map focused on Rad55/Rad57
Rad55-Rad57(E161Q)-SHU-3xRad51 bound to ssDNA with ATP. Local map focused on SHU
Rad55-Rad57(E161Q)-SHU-3xRad51 bound to ssDNA with ATP. Composite map
Rad55-Rad57(E161Q)-SHU-3xRad51 bound to ssDNA with ATP. Local map focused on Rad51
Escherichia coli transcription-translation coupled complex class B (TTC-B) that ribosome walking for 4 codons to a 9 codon mRNA spacer, and fMet-tRNAs in E-site and P-site of the ribosome
PEDV HNXX spike trimer with one D0 Down in complex with one N19 Fab
Focus refinement of PEDV HNXX spike monomer with D0 down in complex with N19 Fab
SARS-CoV-2 BA.3.2.2(RE.2.2) RBD in complex with monoclonal antibodies S2K146 and L4.65
Cryo-EM map of the S1 inner region for the vitreous body collagen fibril at 3.69 angstrom
Cryo-EM structure of human sodium/proton antiporter NHE1 in complex with Zoniporide in an outward-open conformation
Cryo-EM map of the S4 inner region for the vitreous body collagen fibril at 3.24 angstrom
Cryo-EM map of the S3 outer region for the vitreous body collagen fibril at 3.83 angstrom
Cryo-EM map of the S2 outer region for the vitreous body collagen fibril at 5.34 angstrom
Cryo-EM map of the opticin region for the vitreous body collagen fibril at 3.46 angstrom
Cryo-EM map of the S1 outer region for the vitreous body collagen fibril at 5.02 angstrom
Cryo-EM map of the S4 outer region for the vitreous body collagen fibril at 5.37 angstrom
Cryo-EM map of the S2 inner region for the vitreous body collagen fibril at 3.18 angstrom
Cryo-EM map of the S3 inner region for the vitreous body collagen fibril at 3.23 angstrom
Cryo-EM structure of the Crimean-Congo hemorrhagic fever virus full-length L protein RdRP elongation complex (EC14b form)
cryo-EM structure of acetyl-CoA carboxyltransferase holoenzyme dimer from Shewanella oneidensis, mutant E1238A
Cryo-EM structure of the Crimean-Congo hemorrhagic fever virus L protein (apo form)
Cryo-EM structure of the Crimean-Congo hemorrhagic fever virus full-length L protein RdRP elongation complex (EC14 form)
Cryo-EM structure of the Crimean-Congo hemorrhagic fever virus L protein (5'-cRNA-bound form)
D0-state of wild type human mitochondrial LONP1 protease bound to endogenous ADP
Fusion protein of Helicoverpa armigera nucleopolyhedrovirus in the prefusion state
Fusion protein of Helicoverpa armigera nucleopolyhedrovirus in an early fusion intermediate state
Fusion protein of Helicoverpa armigera nucleopolyhedrovirus in the postfusion state
Cryo-EM structure of human pyruvate kinase R (PKR) in complex with an allosteric activator SNH-119014
Cryo-EM structure of inhibitor M353-0039 bound urea transporter A2.
Subtomogram averaging of spike-P17-IgG solo structure on fixed SARS-CoV-2
Subtomogram averaging of SARS-CoV-2 spike-P17-IgG Gemini structure
Subtomogram averaging of SARS-CoV-2 spike-S309-IgG solo structure in 1-RBD-up conformation
Subtomogram averaging of SARS-CoV-2 spike-S309-IgG Gemini structure
Subtomogram averaging of SARS-CoV-2 spike-S309-IgG solo structure in closed conformation
Structure of transposase-activated RAG target capture complex with symmetric linear target DNA (TCC-LS)
Cryo-EM structure of the fiber region of Parabacteroide phage PD491P1
Structure of transposase-activated RAG (RAG1 E962N) target capture complex with disordered U-shaped target DNA (TCC-UD)
Structure of transposase-activated RAG target capture complex with X-form U-shaped target DNA (TCC-UDX)
Structure of transposase-activated RAG strand transfer complex in state 1 (STC-1)
Structure of transposase-activated RAG strand transfer complex in state 2 (STC-2)
Cryo-electron microscopy structure of nanofibers formed by azobenzene peptides.
Type IV-A1 CRISPR effector complex bound to dsDNA and CasDinG - loaded state
Type IV-A1 CRISPR effector complex bound to dsDNA and CasDinG - locked state
Cryo-EM structure of L9-L4 in complex with Plasmodium falciparum circumsporozoite protein (PfCSP)
Type IV-A1 CRISPR effector complex in locked state, consensus map
Cryo-EM structure of L9-F4 in complex with Plasmodium falciparum circumsporozoite protein (PfCSP)
Cryo-EM structure of human VPS34-CI with ADP:MgF3 - composite map
Reconstruction focused at N-heat-ATRIP of ATR-ATRIP-TOPBP1 AAD monomer
Cryo-EM structure of the complete Saccharomyces cerevisiae RNA polymerase II in closed clamp conformation
Cryo-EM structure of the complete Saccharomyces cerevisiae RNA polymerase II in open clamp conformation
Cryo-EM structure of the complete Pyrococcus furiosus RNA polymerase in open clamp conformation
Cryo-EM structure of the complete Pyrococcus furiosus RNA polymerase in closed clamp conformation
Cryo-EM structure of the complete Sulfolobus acidocaldarius RNA polymerase in closed clamp conformation
Cryo-EM structure of the complete Sulfolobus acidocaldarius RNA polymerase in open clamp conformation
Cryo-EM structure of Saccharomyces cerevisiae RNA polymerase II without stalk (no Rpb4/Rpb7)
Cryo-EM structure of Sulfolobus acidocaldarius RNA polymerase without stalk (no Rpo4/Rpo7)
Monomeric ADAR2_E488Q bound to dsRNA sequence derived from human GLI1 gene
Microtubule-associated LRRK2 I2020T filaments in HEK293T cells treated with GZD-824
Cryo-EM structure of Pyrococcus furiosus RNA polymerase without stalk (no Rpo4/Rpo7)
Alternative NBD1-binding geometry in channel-formed, ATP-bound, VX809-bound, T2a-nanobody-bound wild-type human CFTR (sharpened consensus map from cryoSPARC non-uniform refinement)
Cryo-EM density of the [NiFe]-hydrogenase HoxEFU diaphorase subcomplex
Focused map of four central LRRK2 I2020T units in the microtubule-associated filament lattice formed in the presence of MLi-2
Focused map of the COR:COR interaction interface in microtubule-associated LRRK2 I2020T filaments formed in the presence of MLi-2
Alternative NBD1-binding geometry in channel-formed, ATP-bound, VX809-bound, T2a-nanobody-bound wild-type human CFTR (sharpened AHD1 local refinement map from cryoSPARC)
Alternative NBD1-binding geometry in channel-formed, ATP-bound, VX809-bound, T2a-nanobody-bound wild-type human CFTR (sharpened AHD2 local refinement map from cryoSPARC)
Alternative NBD1-binding geometry in channel-formed, ATP-bound, VX809-bound, T2a-nanobody-bound wild-type human CFTR (sharpened CORE1 local refinement map from cryoSPARC)
Alternative NBD1-binding geometry in channel-formed, ATP-bound, VX809-bound, T2a-nanobody-bound wild-type human CFTR (sharpened NBD2 plus T2a local refinement map from cryoSPARC)
Alternative NBD1-binding geometry in channel-formed, ATP-bound, VX809-bound, T2a-nanobody-bound wild-type human CFTR (sharpened CORE2 local refinement map from cryoSPARC)
Alternative NBD1-binding geometry in channel-formed, ATP-bound, VX809-bound, T2a-nanobody-bound wild-type human CFTR (sharpened WalkerB1 local refinement map from cryoSPARC)
Alternative NBD1-binding geometry in channel-formed, ATP-bound, VX809-bound, T2a-nanobody-bound wild-type human CFTR (sharpened WalkerB2 local refinement map from cryoSPARC)
Alternative NBD1-binding geometry in channel-formed, ATP-bound, VX809-bound, T2a-nanobody-bound wild-type human CFTR (sharpened T2a plus T2a local refinement map from cryoSPARC)
Alternative NBD1-binding geometry in channel-formed, ATP-bound, VX809-bound, T2a-nanobody-bound wild-type human CFTR (sharpened NBD1 plus T2a local refinement map from cryoSPARC)
Human respirovirus 3 hemagglutinin-neuraminidase dimer in complex with VHH A2R3-60
Human respirovirus 1 hemagglutinin-neuraminidase dimer in complex with VHH A2R3-60
Human respirovirus 3 hemagglutinin-neuraminidase dimer in complex with VHH A2R3-59
Reconstruction focused at FAT-kinase of symmetric class of ATR-ATRIP-ETAA1 AAD
Consensus reconstruction of symmetric class of ATR-ATRIP-ETAA1 AAD
Reconstruction focused at N-heat-M-heat-FAT of symmetric class of ATR-ATRIP-ETAA1 AAD
Reconstruction focused at N-heat-ATRIP of symmetric class of ATR-ATRIP-ETAA1 AAD
Reconstruction focused at N-heat-ATRIP-M-heat-FAT of open protomer of apo-ATR-ATRIP
Reconstruction focused at N-heat-ATRIP-M-heat-FAT of closed protomer of apo-ATR-ATRIP
Consensus reconstruction of ATR-ATRIP-TOPBP1 AAD (monomer after symmetry expansion and signal subtraction)
Reconstruction focused at N-heat-ATRIP-M-heat-FAT of ATR-ATRIP-TOPBP1 AAD monomer
Reconstruction focused at FAT-kinase of ATR-ATRIP-TOPBP1 AAD monomer
Sub-tomogram averaged structure of E. Coli DNA protection during starvation protein (DPS)
Reconstruction focused at N-heat-ATRIP of ATR-ATRIP-ETAA1 AAD (S95D/S111D)
Reconstruction focused at N-heat-ATRIP-M-heat of open protomer of ATR-ATRIP-ETAA1 AAD (S95D/S111D)
Reconstruction focused at FAT-kinase of ATR-ATRIP-ETAA1 AAD (S95D/S111D)
Reconstruction focused at N-heat-ATRIP-M-heat-FAT of closed protomer of ATR-ATRIP-ETAA1 AAD (S95D/S111D)
Local multi-body refinement of bmCCAN bmCENP-HIK-T dimerization interface, part of the dimeric bmCCAN-DNA complex
Local multi-body refinement of bmCCAN-2, part of the dimeric bmCCAN-DNA complex
Local multi-body refinement of bmCCAN-1, part of the dimeric bmCCAN-DNA complex
CENP-HIK Head domain local refinement for monomeric bmCCAN-DNA complex
Trypanosoma brucei mitochondrial RNA-editing catalytic complex 2, U-insertion (RECC2), left wing focused refinement map
Trypanosoma brucei mitochondrial RNA-editing catalytic complex 2, U-insertion (RECC2), right wing focused refinement map
Trypanosoma brucei mitochondrial RNA-editing catalytic complex 2, U-insertion (RECC2), consensus map
Trypanosoma brucei mitochondrial RNA-editing catalytic complex (RECC), tRNA focused refinement map
Cryo-EM structure of human VPS34-CI with ADP:MgF3 - local refinement on the complex base
Cryo-EM structure of human VPS34-CI in complex with GABARAP, local refinement on VPS15 helical solenoid, and BECLIN1 and ATG14L N-terminal domains.
Cryo-EM structure of human VPS34-CI with ADP:MgF3 - local refinement on ATG14L and BECLIN1 C-termini
Cryo-EM structure of inhibitor E822-1968 bound human urea transporter A2.
Cryo-EM structure of human VPS34-CI with ADP:MgF3 - local refinement on VPS34 and VPS15 kinases
Cryo-EM structure of human VPS34-CI in complex with GABARAP - alternative conformation, composite map
Cryo-EM structure of human VPS34-CI in complex with GABARAP, local refinement on the core of VPS34-CI.
Cryo-EM structure of human VPS34-CI in complex with GABARAP - alternative conformation, consensus map
Cryo-EM structure of human VPS34-CI in complex with GABARAP - alternative conformation, local refinement on BECLIN1 and ATG14L C-terminal domains.
Cryo-EM structure of human VPS34-CI in complex with GABARAP, consensus map
Cryo-EM structure of human VPS34-CI in complex with GABARAP, local refinement on GABARAP.
Cryo-EM structure of human VPS34-CI in complex with GABARAP, composite map
Cryo-EM structure of human VPS34-CI with ADP:MgF3 - consensus map
Cryo-EM structure of human VPS34-CI in complex with GABARAP, local refinement on BECLIN1 and ATG14L C-terminal domains.
Cryo-EM structure of human VPS34-CI in complex with GABARAP, local refinement on VPS34 and VPS15 kinase domains.
PEDV HNXX spike trimer with two D0 down in complex with two N19 Fabs
Cryo-EM structure of the ARISC(E33A)-RAP80:K63-Ub7 complex (Non-catalytic Ub, Left Arm map)
Cryo-EM structure of the ARISC(E33A)-RAP80:K63-Ub7 complex (Non-catalytic Ub, Right Arm map)
Cryo-EM structure of the ARISCdC(E33A):K63-Ub7 complex (Right Arm map)
Cryo-EM structure of the ARISCdC(E33A):K63-Ub7 complex (Ub (P2) and Ub (P3) map)
Cryo-EM structure of the ARISC(E33A)-RAP80:K63-Ub7 complex (Ub (P1') map)
Cryo-EM structure of the ARISCdC(E33A):K63-Ub7 complex (Left Arm map)
Cryo-EM structure of the ARISC(E33A)-RAP80:K63-Ub7 complex (Right Arm map)
Cryo-EM structure of the ARISCdC(E33A):K63-Ub7 complex (Consensus Map)
Cryo-EM structure of the ARISCdC(E33A):K63-Ub7 complex (Ub (P1') map)
Cryo-EM structure of the ARISCdC(E33A):K63-Ub4 complex (Consensus map)
Cryo-EM structure of the ARISC(E33A)-RAP80:K63-Ub7 complex (Consensus Map)
Cryo-EM structure of the ARISCdC(E33A):K63-Ub4 complex (Composite map)
Cryo-EM structure of the ARISCdC(E33A):K63-Ub4 complex (Right Arm map)
Cryo-EM structure of the ARISCdC(E33A):K63-Ub7 complex (Composite map)
Cryo-EM structure of ARISCdC(E33A):K63-Ub4 complex (Ub (P1') map)
Cryo-EM structure of the ARISC(E33A)-RAP80:K63-Ub7 complex (Composite map)
Metabotropic Glutamate Receptor 7 in complex with ecto-domain of Extracellular Leucine Rich Repeat and Fibronectin Type III Domain Containing 2
Structure of holo vanadium-dependent haloperoxidase from Enhygromyxa salina bound to vanadate, and bromide
Structure of vanadium-dependent haloperoxidase from Enhygromyxa salina bound to vanadate, bromide, and hydrogen peroxide
Cryo-EM structure of His6-tagged D13 assembled into scaffold-like particles from vaccinia virus
Two interacting D13 trimers at mode III interface in Twister assembly
Cryo-EM structure of A17(1-16) peptide-bound D13 trimer from vaccinia virus
Structure of the heptameric pre-pore state of alpha-hemolysin in the presence of A549 cells at pH 7
Cryo-EM structure of A17(1-16) peptide-bound D13 assembled into scaffold-like particles from vaccinia virus
Structure of the heptameric pore state of alpha-hemolysin in the presence of A549 cells at pH 5.5
Cryo-EM structure of eGFP-tagged D13 assembled into scaffold-like particles from vaccinia virus
Two interacting D13 trimers at mode II interface in Twister assembly
Subtomogram averaging of in vitro assembly product of untagged D13, Twister
Subtomogram averaging of His6-tagged D13 assembled into scaffold-like particles from vaccinia virus
Two interacting D13 trimers at mode I interface in Twister assembly
Cryo-EM structure of in vitro assembly product of untagged D13, Twister
Cryo-EM structure of the A17(1-16) peptide-bound N-terminal 17 residue truncated D13 trimer from vaccinia virus
Cryo-EM structure of the de novo designed metalloprotease PP507 E110Q mutant
Cryo-EM structure of the de novo designed metalloprotease DP221 E85Q mutant
Cryo-EM structure of the de novo designed metalloprotease DP622 E96Q mutant
Human FATP2 K572A mutant in complex with oleic acids and ATP in pre-catalytic state
In-cell map of electron transport chain supercomplex from T cells of older patients after restimulation by subtomogram averaging
In-cell map of mitoribosome from T cells of middle-aged patients after restimulation by subtomogram averaging
In-cell map of electron transport chain supercomplex from T cells of middle-aged patients after restimulation by subtomogram averaging
In-cell map of mitoribosome from T cells of older patients after restimulation by subtomogram averaging
Tomogram of mitochondria in T cell from middle-aged patients after restimulation