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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Tetrahymena Ribozyme L-16 complex with small molecule inhibitor ZPT-084
Cryo-EM structure of D1R-Gs in complex with de novo designed GEM targetingTM1/2/4 and GEM targeting TM3/4/5, and agonist-positive allosteric GEM targeting TM5/6/7
Cryo-EM structure of D1R-Gs in complex with de novo designed agonist-positive allosteric GEM targeting TM5/6/7
Octamer Msp1 from S.cerevisiae (with a catalytic dead mutation) in complex with an unknown peptide substrate
Cryo-EM structure of D1R in complex with de novo designed negative allosteric GEM targeting TM5/6/7
Structural insights into photosystem I complex of Bryopsis corticulans
Cryo-EM structure of D1R in complex with de novo designed GEM targeting TM1/2/4 and GEM targeting TM3/4/5, and negative allosteric GEM targeting TM5/6/7
Cryo-EM structure of the SARS-CoV-2 spike protein in complex with S416
Cryo-EM structure of D1R-Gs in complex with de novo designed GEM targeting TM1/2/4
Cryo-EM structure of D1R-Gs in complex with de novo designed GEM targeting TM3/4/5
Nonamer Msp1 from S.cerevisiae (with a catalytic dead mutation) in complex with an unknown peptide substrate
Structure of Csm6 from Actinomyces procaprae in complex with cyclic hexa-adenylate
Decamer Msp1 from S.cerevisiae(with a catalytic dead mutation) in complex with an unknown peptide substrate
GFP bound to distal DARPin (AHIR dodecamer scaffold system from split dataset with 5500 micrographs)
GFP bound to distal DARPin (AHIR dodecamer scaffold system from split dataset with 2500 micrographs)
GFP bound to distal DARPin (AHIR dodecamer scaffold system from split dataset with 7500 micrographs)
GFP bound to distal DARPin (AHIR dodecamer scaffold system from split dataset with 11594 micrographs)
GFP bound to distal DARPin (AHIR dodecamer scaffold system from split dataset with 4500 micrographs)
GFP bound to distal DARPin (AHIR dodecamer scaffold system from split dataset with 11500 micrographs)
structure of two human ELF2 transcription factors in complex with a nucleosome
Cryo-EM focus map of prefusion SARS-CoV-2 spike (RBDs: 1 up & 2 down) bound to RBD-targeting MO176-117 antibody
CryoEM map of Intermediate 2 of SARS-CoV-2 spike protein (from revitrified dataset)
Cryo-EM consensus map of prefusion SARS-CoV-2 spike (RBDs: 1 up & 2 down) bound to RBD-targeting MO176-117 antibody
CryoEM map of Intermediate 3 of SARS-CoV-2 spike protein (from revitrified dataset)
GFP bound to distal DARPin (AHIR dodecamer scaffold system from split dataset with 10500 micrographs)
CryoEM map from 60 microseconds revitified sample of SARS-CoV-2 spike protein
CryoEM map of Intermediate 5 of SARS-CoV-2 spike protein (from revitrified dataset)
CryoEM map of Intermediate 4 of SARS-CoV-2 spike protein (from revitrified dataset)
Cryo-EM focus map of prefusion SARS-CoV-2 spike (RBDs: 2 up & 1 down) bound to RBD-targeting MO176-117 antibody
Cryo-EM Structure of Self-assembled Zymomonas mobilis Levansucrase Nanotube
Nitrogenase maturase NifEN in complex with the cofactor chaperone NifX
CryoEM map from 30 microseconds revitified sample of SARS-CoV-2 spike protein
Cryo-EM consensus map of prefusion SARS-CoV-2 spike (RBDs: 2 up & 1 down) bound to RBD-targeting MO176-117 antibody
GFP bound to distal DARPin (AHIR dodecamer scaffold system from split dataset with 6500 micrographs)
GFP bound to distal DARPin (AHIR dodecamer scaffold system from split dataset with 500 micrographs)
GFP bound to distal DARPin (AHIR dodecamer scaffold system from split dataset with 8500 micrographs)
GFP bound to distal DARPin (AHIR dodecamer scaffold system from split dataset with 3500 micrographs)
GFP bound to distal DARPin (AHIR dodecamer scaffold system from split dataset with 9500 micrographs)
Subtomogram average of nucleosomes extracted from vitreous sections of Drosophila melanogaster embryos
Roseiflexus castenholzii cells with contractile injection systems.
Roseiflexus castenholzii cells with contractile injection systems.
Roseiflexus castenholzii cells with contractile injection systems.
Roseiflexus castenholzii cells with contractile injection systems.
Escherichia coli ribosome arrested on a chimeric, 130-residue construct featuring a firefly-luciferase truncation followed by SecM(3W)
Roseiflexus castenholzii cells with contractile injection systems.
Roseiflexus castenholzii cells with contractile injection systems.
Escherichia coli ribosome arrested on a chimeric, 190-residue construct featuring a firefly-luciferase truncation followed by SecM(3W)
Escherichia coli ribosome arrested on a chimeric, 110-residue construct featuring a firefly-luciferase truncation followed by SecM(3W)
Roseiflexus castenholzii cells with contractile injection systems.
Roseiflexus castenholzii cells with contractile injection systems.
Scaffold attached to quinine-I aptamer (Tonic) local refinement of aptamer
RNA scaffold attached to 8-oxoguanine riboswitch aptamer, combined core plus aptamer
Scaffold attached to quinine-I aptamer (Tonic) local refinement of core
Scaffold attached to quinine-I aptamer (Tonic) refinement of aptamer and core
Reconstruction of the intracellular varicella-zoster virus capsid with portal.
Reconstruction of intracellular varicella zoster virus CAI-capsid with portal.
Reconstruction of the varicella-zoster virus C-capsid with the portal vertex.
Reconstruction of the portal vertex from intracellular varicella-zoster virus CAI-capsids.
2'-fluoro-modified pyrimidine (FY) RNA aptamer binding to the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. (focus map: RBD-aptamer)
Scaffold attached to Mango without ligand, local refinement of core, tilted data collection of tetramer
RNA scaffold attached to 8-oxoguanine riboswitch aptamer Glacios data
Scaffold attached to Mango without ligand, local refinement of aptamer, tilted data collection of tetramer
Cryo-EM structure of the CHSY3-CHPF1 chondroitin synthase heterodimer
Structure of the MOR/Gi/DAMGO Complex, GTP-Bound, G-Primed, AHD-Sorted
RNA scaffold attached to 8-oxoguanine riboswitch core Glacios data
RNA scaffold attached to 8-oxoguanine riboswitch aptamer core only
Artemia ferritin cell-free expression with reverse his purification
Human 80S ribosome bound to IDB-002 stalled on FPAK-containing nascent chain
Structure of the MOR/Gi/Mitragynine Pseudoindoxil Complex, GTP-bound G-Primed, Consensus Refinement
Structure of the MOR/Gi/Mitragynine Pseudoindoxil Complex, GTP-bound G-ACT-2/3 Consensus Refinement
Cryo-EM Map of the FtsH.HflK/C Complex Solubilized in DDM from Tobramycin-Treated Cells
Cryo-EM map of the FtsH.HflK/C membrane assembly extracted in carboxy-DIBMA from tobramycin-treated cells
Cryo-EM structure of the engineered HflK/C variant stabilized in the closed conformation via disulfide bond crosslinking.
In situ cryo-electron tomogram of 4days rpn9 surface mutant nucleus
In situ cryo-electron tomogram of 4days glucose control WT nucleus
100 kV cryo-EM structure of apoferritin at 1.91 A with DECTRIS SINGLA detector on CRYO ARM 200 II
Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1G1
In situ cryo-electron tomogram of 4days mlp1delta mlp2delta nucleus
Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1B2
Inward-occluded structure of human GABA transporter 3 bound to substrate GABA
2'-fluoro-modified pyrimidine (FY) RNA aptamer binding to the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. (focus map: PXT origami 'pointer')
2'-fluoro-modified pyrimidine (FY) RNA aptamer binding to the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. (focus map: Spike core)
3-helix origami tile + Broccoli and Pepper aptamers (3HT-BP) with 2'-Fluoro-modified pyrimidines (FY RNA)
2'-fluoro-modified pyrimidine (FY) RNA aptamer binding to the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. (focus map: Spike N-terminal domain (NTD))
2'-fluoro-modified pyrimidine (FY) RNA aptamer binding to the receptor binding domain (RBD) of the SARS-CoV-2 spike protein (Full map, no symmetry)
Cryo-EM structure of mouse heavy-chain apoferritin at 1.24 A on CRYO ARM 200 II
CryoEM structure of delta opioid receptor bound to G proteins and met-enkephalin
CryoEM structure of delta opioid receptor bound to G proteins and Naltrindole
CryoEM structure of delta opioid receptor bound to G proteins and naltrexone
CryoEM structure of delta opioid receptor bound to G proteins and ADL5859
CryoEM structure of delta opioid receptor bound to G proteins and SNC80
CryoEM structure of stabilized dengue 3 virus envelope glycoprotein in complex with Fab of F25.S01
In situ structure of the cardiac thin filament without troponin from MYH7(WT/G256E) human induced pluripotent stem cell-derived cardiomyocytes (AICS-0097-141 ACTN2-mEGFP MYH7(WT/G256E))
In situ structure of the cardiac thin filament without troponin from isogenic control human induced pluripotent stem cell-derived cardiomyocytes (AICS-0097-113 ACTN2-mEGFP MYH7(WT/WT))
In situ structure of the cardiac thin filament without troponin from untreated human induced pluripotent stem cell-derived cardiomyocytes (SCVI-273)
In situ structure of the cardiac thin filament with troponin from MYH7(WT/G256E) human induced pluripotent stem cell-derived cardiomyocytes (AICS-0097-141 ACTN2-mEGFP MYH7(WT/G256E))
In situ structure of the cardiac thin filament without troponin from doxorubicin-treated human induced pluripotent stem cell-derived cardiomyocytes (SCVI-273)
In situ structure of the cardiac thin filament with troponin from untreated human induced pluripotent stem cell-derived cardiomyocytes (SCVI-273)
In situ structure of the cardiac thin filament with troponin from isogenic control human induced pluripotent stem cell-derived cardiomyocytes (AICS-0097-113 ACTN2-mEGFP MYH7(WT/WT))
ln situ structure of the cardiac thin filament with troponin from doxorubicin-treated human induced pluripotent stem cell-derived cardiomyocytes (SCVI-273)
Capsid Subtomogram Average From NL4.3:PR(D25N) Immature HIV-1 Virions
Globally refined map of odorant-bound mouse class II odorant receptor G protein complex
Cryo-EM structure of the large serine recombinase Bxb1 in complex with attP and attB (GT/TT CDN) in the pre-strand exchange state
Cryo-EM structure of the large serine recombinase Bxb1 in complex with attP and attB (GT/TT CDN) in the pre-strand exchange state (attB-R)
Cryo-EM structure of the large serine recombinase Bxb1 in complex with attP and attB (GT/TT CDN) in the pre-strand exchange state (attP-R)
Cryo-EM structure of the large serine recombinase Bxb1 in complex with attP and attB (GT/TT CDN) in the post-strand exchange state
2.62A cryo-EM structure of RNA-directed RNA polymerase L of Crimean-Congo hemorrhagic fever virus (Apo state)
Cryo-EM structure of the large serine recombinase Bxb1 in complex with attP and attB (CA/CA CDN) in the intermediate-strand exchange state 1
The structure of odorant-bound mouse class II odorant receptor-miniGs complex
Cryo-EM structure of the large serine recombinase Bxb1 in complex with attP and attB (GT/TT CDN) in the pre-strand exchange state (attB-L)
Receptor-focused map of odorant-bound mouse class II odorant receptor G protein complex
Cryo-EM structure of the large serine recombinase Bxb1 in complex with attP and attB (CA/CA CDN) in the intermediate-strand exchange state 2
Cryo-EM structure of the large serine recombinase Bxb1 in complex with attP and attB (GT/TT CDN) in the pre-strand exchange state (attP-L)
Cryo-EM structure of the large serine recombinase Bxb1 in complex with attP and attB (CA/CA CDN) in the pre-strand exchange state
Cryo-EM structure of the large serine recombinase Bxb1 in complex with attP and attB (CA/CA CDN) in the post-strand exchange state
2.53A cryo-EM structure of RNA-directed RNA polymerase L of Crimean-Congo hemorrhagic fever virus (RNA bound)
Yeast-expressed polio type 1 stablized virus-like particles with 3G10 Fab
GFP bound to distal DARPin (AHIR dodecamer scaffold system from split dataset with 1500 micrographs)
Ecoli DnaB helicase and Phage Lambda loader P with ADP-Mg in a 6:5 stoichiometry ratio
Transferrin Binding Protein A in complex with transferrin binding protein B and two molecules of transferrin
Transferrin Binding Protein A in complex with transferrin binding protein B and transferrin (iron bound in both lobes of Tf)
Cryo-EM structure of human ATP citrate lyase in complex with inhibitor EVT0185-CoA
Neisseria gonorrhoeae Transferrin Binding Protein A in complex with Transferrin Binding Protein B and transferrin (iron bound in N lobe only)
Structure of the MOR/Gi/Lofentanil Complex, GTP-bound G-ACT-2/3, Global and G Protein Local
Structure of the MOR/Gi/Lofentanil Complex, GTP-bound G-ACT-2', G Protein Local
Structure of the MOR/Gi/Lofentanil Complex, GTP-bound G-ACT-2, G Protein Local
Transferrin Binding Protein A in complex with transferrin binding protein B, transferrin and globular domain of TonB
Structure of the MOR/Gi/Lofentanil Complex, GTP-bound G-ACT-2/3, Global 3DVA Sorted 1
Structure of the MOR/Gi/Lofentanil Complex, GTP-bound G-ACT-2/3, Global 3DVA Sorted 2
Pathogen effector forms a phosphatase holoenzyme complex with host core enzyme to promote disease
Local refinement map of the cytoplasmic lattice (CPL) from mouse oocyte at 3.90 angstrom
Local refinement map of the cytoplasmic lattice (CPL) from mouse oocyte at 3.94 angstrom
Local refinement map of the cytoplasmic lattice (CPL) from mouse oocyte at 3.81 angstrom
Pathogen effector forms a phosphatase holoenzyme complex with host core enzyme to promote disease
Pathogen effector forms a phosphatase holoenzyme complex with host core enzyme to promote disease
Subtomogram average of GEM-mCherry-nanobody particles on A549 cell membranes
Local refinement map of the cytoplasmic lattice (CPL) from mouse oocyte at 3.87 angstrom
Cryo-EM structure of transducer in complex with chimeric receptor
A Cryo-EM structure of LA-PTH-PTH1R-V2RT-Beta-arrestin1 complex (state 1 conformation)
Pathogen effector forms a phosphatase holoenzyme complex with host core enzyme to promote disease
A Cryo-EM structure of LA-PTH-PTH1R-V2R-Beta-arrestin1 complex (state 2 conformation)
Local refinement map of the cytoplasmic lattice (CPL) from mouse oocyte at 4.15 angstrom
A Cryo-EM structure of LA-PTH-PTH1R-B-arrestin1 complex (state 2 conformation)
A Cryo_EM structure of LA_PTH_PTH1R_V2R_Beta_arrestin1 complex(state 2 conformation)
A focused Cryo_EM structure of LA_PTH_PTH1R_V2R_Beta_arrestin1 complex(state 1 conformation)
A focused refinement Cryo_EM structure of A Cryo_EM structure of LA_PTH_PTH1R and V2R_Beta_arrestin1(state 2 conformation)
A Cryo_EM structure of LA_PTH_PTH1R_V2R_Beta_arrestin1 complex(state 1 conformation)
human Argonaute-2 R315V/H316A - miR-122 in complex with a fully complementary target
Structure of human serotonin transporter bound to small molecule zPZd in lipid nanodisc and NaCl
Locally-refined Mu-Opioid Receptor bound with novel compound 0505
Barbed End of Cofilin-2 F-actin, Terminal Actins Occupied with Cofilin
Rhesus rotavirus (consensus structure at 4.7 Angstrom resolution from cryo-ET)
Cryo-EM structure of human dopamine transporter in complex with centanafadine
Structure of Csm6 from Actinomyces procaprae in complex with cyclic penta-adenylate
Cryo-EM structure of human dopamine transporter in complex with tesofensine
Cryo-EM structure of human dopamine transporter in complex with nefazodone
Cryo-EM structure of human dopamine transporter in complex with dasotraline
Cryo-EM structure of human dopamine transporter in complex with ansofasine