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
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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Cryo-tomogram of COPI and COPII vesicles and buds from FIB-milled RPE-1 cells.
Cryo-EM model of E. coli aspartate transcarbamoylase in the ligand-free T-state
Cryo-EM model of E. coli aspartate transcarbamoylase in an expanded state complexed with CP, ATP, GTP, and Mg2+
Cryo-EM model of E. coli aspartate transcarbamoylase in the R-state complexed with CP, succinate, CTP, and Mg2+
Cryo-EM model of E. coli aspartate transcarbamoylase in the R-state complexed with CP, succinate, ATP, and Mg2+
Cryo-EM model of E. coli aspartate transcarbamoylase in the T-state complexed with CP, ATP, and Mg2+
Cryo-EM model of E. coli aspartate transcarbamoylase in the R-state complexed with CP and succinate
Cryo-EM model of E. coli aspartate transcarbamoylase in the T-state complexed with CP, CTP, UTP, and Mg2+
Cryo-EM model of E. coli aspartate transcarbamoylase in the R-state complexed with CP, succinate, ATP, GTP, and Mg2+
Cryo-EM model of E. coli aspartate transcarbamoylase in the R-state complexed with CP, succinate, CTP, UTP, and Mg2+
Cryo-EM structure of lysophosphatidylserine (18:0)-bound GPR174-Gs complex
Cryo-EM structure of the ATP-bound human mitochondrial Hsp60 C6 complex at 2.83 angstrom resolution from Biortus
Cryo-EM structure of the ATP-bound human mitochondrial Hsp60 C7 complex from Biortus
Cryo-EM structure of native mitochondrial Hsp60 D7 complex from Biortus
Low resolution single particle cryo-EM reconstruction of the HIV-1 Rev/RRE (355 nt)
A cryo-EM structure of B. oleracea RNA polymerase V in complex with 3U sacffold at 3.8 Angstrom
The cryo-EM structure of Pakpunavirus P7-1 head(capsid:decoration protein)
A cryo-EM structure of B. oleracea RNA polymerase V in complex with 0U scaffold at 2.96 Angstrom
The cryo-EM structure of Pakpunavirus P7-1 short tail fiber (gp92) bound to the extended baseplate
RNA polymerase II elongation complex stalled at SHL(-4) of the H3-H4 octasome
The cryo-EM structure of Pakpunavirus P7-1 baseplate in extended status
A cryo-EM structure of B. oleracea RNA polymerase V in complex with 4U sacffold at 3.32 Angstrom
A cryo-EM structure of B. oleracea RNA polymerase V in complex with 1U sacffold at 3.5 Angstrom
RNA polymerase II elongation complex stalled at SHL(-0.5) of the H3-H4 octasome (tetrasome)
A cryo-EM structure of B. oleracea RNA polymerase V in complex with 2U sacffold at 3.04 Angstrom
A cryo-EM structure of B. oleracea RNA polymerase V in complex with 8U sacffold at 4.06 Angstrom
The cryo-EM structure of Pakpunavirus P7-1 neck (portal:H-t-T:collar:gateway)
A cryo-EM structure of B. oleracea RNA polymerase V in complex with 6U sacffold at 3.04 Angstrom
A cryo-EM structure of B. oleracea RNA polymerase V in complex with 7U sacffold at 3.42 Angstrom
In vitro reconstituted complex of purified S. pombe large ribosomal subunit and SNOR
A cryo-EM structure of B. oleracea RNA polymerase V in complex with 5U sacffold at 3.19 Angstrom
The cryo-EM structure of Pakpunavirus P7-1 triplex protein and sheath in contracted state
Structure of the Measles Virus Fusion Glycoprotein Ectodomain in Prefusion Conformation Bound to Neutralizing Antibody H8
Structure of the Measles virus Fusion glycoprotein ectodomain in complex with neutralizing antibody Y10F
Structure of the Measles Virus Fusion Glycoprotein Ectodomain in Postfusion Conformation Bound to Neutralizing Antibody H8
Structure of the Measles virus Fusion glycoprotein ectodomain in complex with two neutralizing antibodies mAb77 and Y10F
Cryo-ET of FIB-milled synapse region between CD19+ NALM6 leukemia cells and T-cells expressing 8H8 CD19 CAR construct, (sample 1), applying a Matlab-based deconvolution filter
Cryo-ET of FIB-milled synapse region between CD19+ NALM6 leukemia cells and T-cells expressing 8H8 CD19 CAR construct, (sample2, region2), applying a Matlab-based deconvolution filter
Cryo-ET of FIB-milled synapse region between CD19+ NALM6 leukemia cells and T-cells expressing 8H8 CD19 CAR construct, (sample2, region3), applying a Matlab-based deconvolution filter
Flavobacterium johnsoniae 70S initiation complex with Shine-Dalgarno-less mRNA.
Flavobacterium johnsoniae bS6 C-terminal deletion mutant 70S ribosome.
Flavobacterium johnsoniae 70S initiation complex with rpsU mRNA containing Shine-Dalgarno sequence. State 1.
Flavobacterium johnsoniae 70S initiation complex with rpsU mRNA containing Shine-Dalgarno sequence. State 2.
Flavobacterium johnsoniae ZAM64 mutant 70S initiation complex with rpsU mRNA containing Shine-Dalgarno sequence.
Ubiquinol Binding Site of Cytochrome bo3 from Acinetobacter baumannii
The structure of type III CRISPR-associated deaminase in complex cA6 and ATP, state 3
The structure of type III CRISPR-associated deaminase in complex cA6 and ATP, state 4
The structure of type III CRISPR-associated deaminase in complex cA6 and ATP, state 5
Cryo-EM structure of hepatic amyloid fibril from a variant ATTRV122delta, single filament morphology
Structure of the human 20S proteasome in complex with a beta5-selective covalent syringolin analogue inhibitor.
Native structure of the cytoplasmic lattice filament from mouse MII eggs
Structure of the Plasmodium falciparum 20S proteasome in complex with a beta5-selective covalent syringolin analogue inhibitor.
Structure of the A2058-dimethylated Staphylococcus aureus 70S ribosome complexed with clincelin
Cryo-EM structure of the SN230G6 Fab - HLA-A*02:01 human alloantibody-HLA complex
EM structure of Rec-controlled histidine kinase LvrB, BeF3-activated
Structure of the wild-type Staphylococcus aureus 70S ribosome complexed with clincelin
Cryo-EM structure of the WIM8E5 Fab - HLA-A*11:01 human alloantibody-HLA complex
Composite map of collagenase H (E416Q mutant) from Hathewaya histolytica in complex with collagen model peptide (Pro-Hyp-Gly)12
Cryo-EM map of collagenase H (E416Q mutant) from Hathewaya histolytica in complex with collagen model peptide (Pro-Hyp-Gly)12 - focused map of the Peptidase-Helper-PKD1 domains
Cryo-EM map of collagenase H (E416Q mutant) from Hathewaya histolytica in complex with collagen model peptide (Pro-Hyp-Gly)10 - focused map of ColH bound to the N-terminal region of collagen model peptide
Composite map of collagenase H (E416Q mutant) from Hathewaya histolytica in complex with collagen model peptide (Pro-Hyp-Gly)10
Consensus map of collagenase H (E416Q mutant) from Hathewaya histolytica in complex with collagen model peptide (Pro-Hyp-Gly)12
Cryo-EM map of collagenase H (E416Q mutant) from Hathewaya histolytica in complex with collagen model peptide (Pro-Hyp-Gly)10 - focused map of ColH bound to the C-terminal region of collagen model peptide
Consensus map of collagenase H (E416Q mutant) from Hathewaya histolytica in complex with collagen model peptide (Pro-Hyp-Gly)10
Cryo-EM map of apo collagenase H from Hathewaya histolytica - focused map of the ARM domain
Cryo-EM structure of collagenase H (E416Q mutant) from Hathewaya histolytica bound to C-terminal region of the collagen-binding protein ColH (Pro-Pro-Gly)10
Cryo-EM map of collagenase H (E416Q mutant) from Hathewaya histolytica bound to C-terminal region of collagen model peptide (Pro-Hyp-Gly)10
Cryo-EM map of apo collagenase H from Hathewaya histolytica - focused map of the Peptidase-Helper-PKD1 domains
Severed and capped actin fragment by two G1G3 domains of gelsolin
Cryo-EM map of collagenase H (E416Q mutant) from Hathewaya histolytica in complex with collagen model peptide (Pro-Hyp-Gly)12 - focused map of the ARM domain
Cryo-EM structure of BA1-1-bound alpha-synuclein fibril polymorph 6A6B
Cryo-EM structure of HA11-bound alpha-synuclein fibril polymorph 6A6B
Cryo-EM structure of BA22-bound alpha-synuclein fibril polymorph 6A6B
Cryo-EM structure of BA23-bound alpha-synuclein fibril polymorph 6A6B
Cryo-EM structure of Integrin alpha V beta 6 complex with a bicyclic inhibitory peptide
Cryo-EM structure of HA32-bound alpha-synuclein fibril polymorph 6A6B
Cryo-EM structure of BA12-bound alpha-synuclein fibril polymorph 6A6B
Cryo-EM structure of HA21-bound alpha-synuclein fibril polymorph 6A6B
Cryo-EM structure of BA21-bound alpha-synuclein fibril polymorph 6A6B
Cryo-EM structure of HA31-bound alpha-synuclein fibril polymorph 6A6B
RAD51-ssDNA filament in complex with calcium and ATP bound by the RAD54 N-terminus
CryoEM structure of Arabidopsis TIR-NLR WRR4A tetramer in complex with effector CCG40 (focused refinement)
RAD51-dsDNA filament in complex with calcium and ATP bound by the RAD54B N-terminus
Structure of the type IV pilus machinery from Thermus thermophilus in the closed state (C6 symmetry)
Consensus Map of the Peptide-Loading Complex Arrested by HCMV US6
RAD51-ssDNA filament in complex with magnesium and ATP bound by the RAD54B N-terminus (beta-barrel)
RAD51-ssDNA filament in complex with magnesium and ATP bound by the RAD54B N-terminus (peptide)
RAD51-ssDNA filament in complex with calcium and ATP bound by the RAD54B N-terminus
Structure of piperidine-4-sulfonic acid-bound human Taurine Transporter in the inward-open conformation
Structure of human apo Taurine Transporter in the inward-occluded conformation
Structure of taurine-bound human Taurine Transporter in the inward-occluded conformation
Structure of human apo Taurine Transporter in the inward-open conformation
Structure of beta-alanine-bound human Taurine Transporter in the inward-occluded conformation
Structure of piperidine-4-sulfonic acid-bound human Taurine Transporter in the inward-occluded conformation
Structure of the Argonaute protein from Verrucomicrobiota bacterium in complex with guide DNA and target RNA in dimeric state.
The transition-state structure of the Argonaute protein from a Verrucomicrobia bacterium in complex with guide DNA and target RNA.
Structure of the Argonaute protein from Verrucomicrobia bacterium in complex with guide DNA and target RNA in monomeric state.
Structure of the Argonaute protein from Verrucomicrobia bacterium in complex with guide DNA and target RNA in monomeric state.
Structural basis for the assembly and translocation of the Vip1-Vip2 insecticidal binary toxin from Bacillus thuringiensis
Structure of the Argonaute protein from Verrucomicrobia bacterium in complex with guide DNA and target RNA
Structural basis for the assembly and translocation of the Vip1-Vip2 insecticidal binary toxin from Bacillus thuringiensis
Structural basis for the assembly and translocation of the Vip1-Vip2 insecticidal binary toxin from Bacillus thuringiensis
Structure of the Argonaute protein from Verrucomicrobia bacterium in complex with guide DNA
Structure of the Argonaute protein from Verrucomicrobia bacterium in complex with guide DNA and target RNA in target-released state
Cryo-EM structure of the endogenous U2/branchpoint spliceosomal complex (core)
Cryo-EM structure of the endogenous U2/branchpoint spliceosomal complex (SF3A state 1)
Cryo-EM structure of the endogenous U2/branchpoint spliceosomal complex (SF3A state 2)
Cryo-EM structure of the endogenous U2/branchpoint spliceosomal complex (Distal DHX15 state)
Cryo-EM structure of the endogenous U2/branchpoint spliceosomal complex (Proximal DHX15 state)