EMDB Search Engine documentation
Text Search
You can use the search bar near the top of all EMDB pages to search across any data deposited at EMDB and EMPIAR.
The EMDB search engine was built using the Apache Solr server, therefore you can check the Solr query parser tutorial to find further information about how to use this engine. You can also check the full list of EMDB query fields.
Query Syntax
Free text terms
Most of the text fields are broken up into single words before indexing. This procedure allows you to perform searches based on single terms or phrases (using double quotes).
The search below returns all the entries that contain the word "zika" anywhere:
The search below returns all the entries that contain the phrase "monoclonal antibody" anywhere:
Boolean operators
More complex queries can be created by combining multiple terms and boolean operators.
| Boolean operator | Description | Example |
|---|---|---|
| AND | Both terms are required. | spliceosome AND human |
| OR | One of the terms is required. | spliceosome OR ribonucleoprotein |
| NOT | The following term must not be present. | NOT Relion |
The search terms can be grouped to form sub-queries and parentheses are used to define the order of the sub-queries. The query below returns all entries that contain the words spliceosome or ribonucleoprotein, but do not contain the word human.
"(spliceosome OR ribonucleoprotein) AND NOT human"
Search by specific fields
Searching by specific fields allows the user to obtain more confident results. All you need to do is specify the field followed by a colon (":") and the term that you are searching for within the field. All the query syntax previously described is also available for specific-field searches. The full list of fields and their description can be found here.
An example to find all the human spliceosomes or ribonucleoproteins, using the sample name and the human taxonomy ID: 9606:
(sample_name:ribonucleoprotein OR sample_name:spliceosome) AND natural_source_ncbi_code:9606
Range Search
The search egnine allows the user to find entries that fall within a given range. The upper and lower bounds must be provided in the following format: "[X TO Y]". The example below finds all entries with a resolution value between 1Å and 3Å.
You can also use curly brackets to set exclusive range intervals. In the example below we are retrieving all entries with resolution value between 1Å and 3Å, but excluding entries with exactly 3Å resolution.
Range queries are not restricted to numeric fields, it is possible to search over date and text ranges. You can find the Solr documentation about date formats here. The example below returns all entries that contain samples starting with the letter "X", "Y" or "Z".
An asterisk ("*") can be used as to match any values. It can be included in a range query to define an infinite interval. The example below finds all entries with resolution value greater than or equal to 20Å.
Another use of the asterisk is to match every entry that has a value for that field. The example below list all entries that contain half-maps:
Fuzzy Search
The EMDB search engine allows the user to search by similar terms using the Damerau-Levenshtein Distance (basically, the number of edit operations necessary to transform one string in another). To perform a fuzzy search, you need to add the tilde symbol ("~") after the query term followed by the maximum distance. The example below will match any sample term that is at most one text edit from the word DNA. In other words, it will return all entries containing samples of DNA or RNA.
Quick links
Recent Entries
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Structural basis for the nucleosome binding and chromatin compaction by the linker histone H5
multidrug transporter EfpA from Mycobacterium tuberculosis bound with lipids
Cryo-EM structure of SUCR1 in complex with cis-epoxysuccinic acid and Gi proteins
Cryo-EM structure of the Ycf2-FtsHi motor complex from Arabidopsis in Apo state
Cryo-EM structure of the Ycf2-FtsHi motor complex from chlamydomonas reinhardtii in apo state
Cryo-EM structure of the Ycf2-FtsHi motor complex from Chlamydomonas reinhardtii in AMPPNP bound state
Structural basis for the nucleosome binding and chromatin compaction by the linker histone H5
Cryo-EM map of the Ycf2-FtsHi motor complex from Chlamydomonas in ATP-bound state
CryoEM structure of non-structural protein 1 dimer from Yellow Fever Virus
Composite map of the Ycf2-FtsHi motor complex from Arabidopsis in apo state
Structural basis for the linker histone H5-nucleosome binding and chromatin compaction
Local EM map of the AtYcf2-FtsHi motor complex in the inter-membrane space region (Apo dataset)
Cryo-EM structure of SUCR1 in complex with succinate and Gi protein
CryoEM structure of non-structural protein 1 tetramer from Yellow Fever Virus
Overall map of the Ycf2-FtsHi motor complex from Arabidopsis in ATP-bound state
Cryo-EM structure of human norepinephrine transporter NET bound with reboxetine in an outward-open state at a resolution of 2.5 angstrom
Cryo-EM structure of human norepinephrine transporter NET bound with norepinephrine in an inward open state at a resolution of 2.5 angstrom
Local refinement of anti-phage defense associated DSR2 tetramer (H171A)
Focused map for area 2 of MapSPARTA tetramer bound with guide-target
Focused map for area 4 of MapSPARTA tetramer bound with guide-target
Focused map for area 3 of MapSPARTA tetramer bound with guide-target
The Cryo-EM structure of anti-phage defense associated DSR2 tetramer bound with two DSAD1 inhibitors (same side)
Cryo-EM structure of anti-phage defense associated DSR2 tetramer (H171A)
The Cryo-EM map of anti-phage defense associated DSR2 tetramer (H171A)
Focused map for area 1 of MapSPARTA tetramer bound with guide-target
The Cryo-EM map of DSR2 tetramer bound with two DSAD1 inhibitor on the same side before local refinement
Cryo-EM structure of anti-phage defense associated DSR2 (H171A) (map2)
Cryo-EM structure of human norepinephrine transporter NET bound with norepinephrine in an occluded state at a resolution of 2.6 angstrom
The Cryo-EM map of DSR2-DSAD1 complex (cross-linked) before local refinement
The Cryo-EM structure of anti-phage defense associated DSR2 tetramer bound with two DSAD1 inhibitors (opposite side)
Local refinement of anti-phage defense associated DSR2 tetramer (H171A)
Local refinement of DSR2 tetramer bound with two DSAD1 inhibitor on the same side
Local refinement of DSR2 tetramer bound with two DSAD1 inhibitor on the same side
Local refinement of anti-phage defense associated DSR2 (H171A) (map2)
The early intermediate structure of baculovirus fusion protein GP64
The Cryo-EM map of anti-phage defense associated DSR2 (H171A) before local refinement (map2)
Cryo-EM structure of human norepinephrine transporter NET bound with atomoxetine in an outward-open state at a resolution of 2.4 angstrom
The cryo-EM map of DSR2-tail tube-NAD complex before local refinement
mus musculus heart thin filament with myosin heads from SOLIST lamellas
Anti-feeding prophage with Afp18DC8 (half of Afp18, N-terminal half) toxin
E.coli gyrase holocomplex with cleaved chirally wrapped 217 bp DNA fragment and moxifloxacin
Pseudo-symmetrical influenza B polymerase apo-dimer, core-only moeity (from "Influenza B polymerase pseudo-symmetrical dimer" | Local refinement)
Anti-feeding prophage with Afp18DC8-Casphi2 toxin-effector chimera
Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-eIF1)
Respiratory complex I from Paracoccus denitrificans in MSP2N2 nanodiscs (ND4 & ND5 focus refinement)
Structure of a eukaryotic replisome stalled at a lagging-strand Topoisomerase 1 cleavage complex with Tof1-Csm3
Influenza polymerase A/H7N9-4M replicase minus 627(R) (from "Influenza polymerase A/H7N9-4M replication complex" | Local refinement)
Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-eIF5)
Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-2)
Pseudo-symmetrical influenza B polymerase apo-dimer, ENDO(T) moiety (from "Influenza B polymerase pseudo-symmetrical dimer" | Local refinement)
CryoEM structure of mTORC1 with a paediatric kidney cancer-associated 1455-EWED-1458 duplication in mTOR, Focused on one protomer copy.
Influenza B polymerase, encapsidase plus 627(R) / human ANP32A (from "Influenza B polymerase apo-trimer" | Local refinement)
Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-3.1)
Influenza B polymerase, replication complex, an asymmetric polymerase dimer bound to human ANP32A (from "Influenza B polymerase apo-trimer" | Local refinement)
Anti-feeding prophage with Afp18DC8-Casphi2 toxin-effector chimera
CryoEM structure of mTORC1 with a paediatric kidney cancer-associated 1455-EWED-1458 duplication in mTOR, overall refinement
Consensus density for neck and tail of phage 812 after tail contraction (C6)
Pseudo-symmetrical influenza B polymerase apo-dimer, ENDO(R) moiety (from "Influenza B polymerase pseudo-symmetrical dimer" | Local refinement)
Structure of the plasma coagulation Factor XIII A2B2 heterotetrameric complex.
Open conformation of the pentameric ligand-gated ion channel, DeCLIC at pH 5 with 10mM EDTA
Closed conformation of the pentameric ligand-gated ion channel, DeCLIC at pH 5 with 10 mM Ca2+
Anti-feeding prophage with Afp18DC8-Casphi2 toxin-effector chimera
Structure of a eukaryotic replisome stalled at a leading-strand Topoisomerase 1 cleavage complex.
Pseudo-symmetrical influenza B polymerase apo-dimer, encapsidase moiety (from "Influenza B polymerase pseudo-symmetrical dimer" | Local refinement)
Open conformation of the pentameric ligand-gated ion channel, DeCLIC at pH 5 with 10mM Ca2+
Cryo-EM structure of Vipp1-deltaH6_aa1-219 helical filament with lattice 3 (Vipp1-deltaH6_L3)
Respiratory complex I from Paracoccus denitrificans in MSP2N2 nanodiscs
Anti-feeding prophage with Afp18DC8-Casphi2 toxin-effector chimera
Structure of a eukaryotic replisome stalled at a lagging-strand Topoisomerase 1 cleavage complex missing Tof1-Csm3.
Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-2.2)
Influenza polymerase A/H7N9-4M replication complex, an asymmetric polymerase dimer bound to human ANP32A
Pseudo-symmetrical influenza B polymerase apo-dimer, ENDO(E) moiety (from "Influenza B polymerase pseudo-symmetrical dimer" | Local refinement)
Cryo-EM structure of Vipp1-F197K/L200K helical filament with lattice 1 (Vipp1-F197K/L200K_L1)
Influenza B polymerase, replicase (from "Influenza B polymerase apo-trimer" | Local refinement)
Structure of the DNase I- and phalloidin-bound pointed end of F-actin (conformer 1)
Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-2.1)
Closed and disordered conformation of the pentameric ligand-gated ion channel, DeCLIC at pH 5 with 10mM EDTA
CryoEM structure of mTORC1 with a paediatric kidney cancer-associated 1455-EWED-1458 duplication in mTOR, Focused region of mTOR and RAPTOR on one protomer copy.
Low resolution cryo-EM structure of FHF bound to KIF1C stalk Hook3 binding domain
Structure of the DNase I- and phalloidin-bound pointed end of F-actin (conformer 2).
Influenza B polymerase, monomeric encapsidase with 5' cRNA hook bound
Influenza polymerase A/H7N9-4M encapsidase plus 627(R) / human ANP32A (from "Influenza polymerase A/H7N9-4M replication complex" | Local refinement)
Anti-feeding prophage with Afp18DC4 toxin (half of Afp18, N-terminal half)
Structure of a yeast 48S-AUC preinitiation complex in closed conformation (model py48S-AUC-3.2)
Cryo-EM structure of the phalloidin-bound pointed end of the actin filament.
Towards the Visual Proteomics of C. reinhardtii using High-throughput Collaborative in situ Cryo-ET : Representative Tomogram
Structure of a yeast 48S-AUC preinitiation complex in closed conformation
Cryo-EM structure of hexameric BTB domain of Drosophila CG6765 protein
Influenza B polymerase pseudo-symmetrical apo-dimer (FluPol(E)|FluPol(S))
High resolution structure of the coagulation Factor XIII A2B2 heterotetramer complex.
MT145KdV5 Env SOSIP in complex with polyclonal Fabs from NHP RM44092 (gp41 epitope)
GT1.1 SOSIP in complex with wk39 polyclonal antibodies from NHP DC8G (V1V2V3 and gp120GH epitopes)
GT1.1 SOSIP in complex with wk39 polyclonal antibodies from NHP A12N030 (gp41GH/FP and base epitopes)
Structure of ecarin from the venom of Kenyan saw-scaled viper in complex with the Fab of neutralizing antibody H11
Lassa GPC (strain Josiah) bound to rabbit polyclonal fusion-peptide-targeting antibody FP-1
GT1.1 SOSIP in complex with wk39 polyclonal antibodies from NHP A12N030 (CD4bs, C3V5 and base epitopes)
Human polymerase epsilon bound to PCNA and DNA in the nucleotide exchange state
Lassa GPC (strain Josiah) bound to rabbit polyclonal base-targeting antibody Base-1
BG505.664 Env SOSIP in complex with polyclonal antibodies from NHP 8147 (C3/V5, V1/V2/V3 apex, gp41 glycan hole/fusion peptide and trimer base epitopes)
Cryo-EM structure of DNMT3A1 UDR in complex with H2AK119Ub-nucleosome
Representative cryo electron tomography reconstructions showing central pair microtubule misalignment in TbArl3A and TbArl3C dual RNAi cells.
Subtomogram averaging of Bxb1 phage tail tip complex during the infection state
Cryo-EM structure of dexmedetomidine-bound alpha-2A-adrenergic receptor in complex with heterotrimeric Gi-protein
Human liver phosphofructokinase-1 filament in the T-state conformation
MT145K Env SOSIP in complex with polyclonal Fabs from NHP RM T923
BG505.664 Env SOSIP in complex with polyclonal antibodies from NHP 8131 (gp120-gp120 interface epitope)
Representative cryo electron tomography reconstructions showing central pair microtubule alignment in a wild type Trypanosoma brucei cell
Subtomogram average of the HN-F complex on the viral surface of an HPIV3 escape variant (EV1).
Human polymerase epsilon bound to PCNA and DNA in the nucleotide bound state
Cryo-EM Structure of E.coli produced recombinant N-acetyltransferase 10 (NAT10) in complex with cytidine-amide-CoA bisubstrate probe and ADP.
Subtomogram average of the HN-F complex on the viral surface of an HPIV3 escape variant (EV2).
Subtomogram average of the HN-F complex on the viral surface of an HPIV3 escape variant mutation (F-L234F).
Cryo-EM structure of epinephrine-bound alpha-2A-adrenergic receptor in complex with heterotrimeric Gi-protein
MT145KdV5 Env SOSIP in complex with polyclonal Fabs from NHP RM44092 (C3/V5 epitope)
BG505.664 Env SOSIP in complex with polyclonal antibodies from NHP 8147 (gp120 glycan hole epitope)
The secreted adhesin EtpA of Enterotoxigenic Escherichia coli in complex with the mouse mAb 1C08
Cryo-EM Structure of E.coli produced recombinant N-acetyltransferase 10 (NAT10) in complex with cytidine-acetone-CoA bisubstrate probe
MT145KdV5 Env SOSIP in complex with polyclonal Fabs from NHP RM44092 (apex V1/V2 epitope)
Cryo-EM Structure of Sf9 produced recombinant N-acetyltransferase 10 (NAT10) in complex with cytidine-amide-CoA bisubstrate probe and ADP/Mg2+.
BG505.664 SOSIP in complex with polyclonal antibodies from NHP 8131 (gp120 glycan hole, gp41 glycan hole/fusion peptide and trimer base epitopes)
GT1.1 SOSIP-CC2 in complex with wk80 polyclonal antibodies from NHP 8229 (V1V2V3, C3V5, CD4bs, gp41GH/FP and base epitopes)
GT1.1 SOSIP in complex with wk39 polyclonal antibodies from NHP DC8G (gp120GH and base epitopes)
GT1.1 SOSIP-CC2 in complex with wk80 polyclonal antibodies from NHP 8239 (gp120GH, gp41GH/FP, CD4bs, and base epitopes)
GT1.1 SOSIP in complex with wk39 polyclonal antibodies from NHP DC8G (gp41GH/FP and gp120GH epitopes)
Cryo-EM structure of the inner MKLN1 dimer from an autoinhibited MKLN1 tetramer
Local EM map of the AtYcf2-FtsHi motor complex in the inter-membrane space region (ATP dataset)
The composite EM map of the Ycf2-FtsHi motor complex from Arabidopsis in ATP-bound state
CryoEM Structure of 40-Residue Arctic (E22G) Beta-Amyloid Fibril Derived by Co-Analysis with Solid-State NMR | E22G Abeta40