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- PDB-7d7m: Cryo-EM Structure of the Prostaglandin E Receptor EP4 Coupled to ... -

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Basic information

Entry
Database: PDB / ID: 7d7m
TitleCryo-EM Structure of the Prostaglandin E Receptor EP4 Coupled to G Protein
Components
  • (Guanine nucleotide-binding protein ...) x 3
  • Prostaglandin E2 receptor EP4 subtype,Prostaglandin E2 receptor EP4 subtype
  • nanobody Nb35
KeywordsMEMBRANE PROTEIN / prostaglandin E receptor / EP4 / GPCR / G protein
Function / homology
Function and homology information


negative regulation of eosinophil extravasation / prostaglandin E receptor activity / negative regulation of integrin activation / Prostanoid ligand receptors / T-helper cell differentiation / regulation of stress fiber assembly / negative regulation of cytokine production / adenylate cyclase-activating G protein-coupled bile acid receptor signaling pathway / adenylate cyclase-activating serotonin receptor signaling pathway / regulation of skeletal muscle contraction ...negative regulation of eosinophil extravasation / prostaglandin E receptor activity / negative regulation of integrin activation / Prostanoid ligand receptors / T-helper cell differentiation / regulation of stress fiber assembly / negative regulation of cytokine production / adenylate cyclase-activating G protein-coupled bile acid receptor signaling pathway / adenylate cyclase-activating serotonin receptor signaling pathway / regulation of skeletal muscle contraction / PKA activation in glucagon signalling / hair follicle placode formation / developmental growth / intracellular transport / D1 dopamine receptor binding / response to mechanical stimulus / vascular endothelial cell response to laminar fluid shear stress / renal water homeostasis / activation of adenylate cyclase activity / Hedgehog 'off' state / adenylate cyclase-activating adrenergic receptor signaling pathway / cellular response to acidic pH / JNK cascade / ERK1 and ERK2 cascade / cellular response to glucagon stimulus / intracellular glucose homeostasis / adenylate cyclase activator activity / positive regulation of insulin secretion involved in cellular response to glucose stimulus / positive regulation of cytokine production / trans-Golgi network membrane / negative regulation of inflammatory response to antigenic stimulus / response to prostaglandin E / cellular response to mechanical stimulus / bone development / platelet aggregation / negative regulation of inflammatory response / cognition / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G-protein beta/gamma-subunit complex binding / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G protein-coupled acetylcholine receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / positive regulation of insulin secretion / positive regulation of inflammatory response / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / photoreceptor disc membrane / ADP signalling through P2Y purinoceptor 12 / sensory perception of smell / Sensory perception of sweet, bitter, and umami (glutamate) taste / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / G alpha (z) signalling events / cellular response to catecholamine stimulus / ADP signalling through P2Y purinoceptor 1 / ADORA2B mediated anti-inflammatory cytokines production / G beta:gamma signalling through PI3Kgamma / adenylate cyclase-activating dopamine receptor signaling pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / cellular response to prostaglandin E stimulus / heterotrimeric G-protein complex / G-protein beta-subunit binding / G alpha (12/13) signalling events / Inactivation, recovery and regulation of the phototransduction cascade / positive regulation of cold-induced thermogenesis / extracellular vesicle / sensory perception of taste / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Thrombin signalling through proteinase activated receptors (PARs) / signaling receptor complex adaptor activity / positive regulation of cytosolic calcium ion concentration / retina development in camera-type eye / GTPase binding / G protein activity / fibroblast proliferation / Ca2+ pathway / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / G alpha (i) signalling events / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Ras protein signal transduction / cell population proliferation / Extra-nuclear estrogen signaling / immune response / G protein-coupled receptor signaling pathway
Similarity search - Function
Prostanoid EP4 receptor / Prostaglandin DP receptor / Prostanoid receptor / G-protein alpha subunit, group S / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G protein alpha subunit, helical insertion / G protein alpha subunit / Guanine nucleotide binding protein (G-protein), alpha subunit ...Prostanoid EP4 receptor / Prostaglandin DP receptor / Prostanoid receptor / G-protein alpha subunit, group S / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G protein alpha subunit, helical insertion / G protein alpha subunit / Guanine nucleotide binding protein (G-protein), alpha subunit / G-protein alpha subunit / G-alpha domain profile. / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / WD domain, G-beta repeat / P-loop containing nucleotide triphosphate hydrolases / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-P2E / Prostaglandin E2 receptor EP4 subtype / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsNojima, S. / Fujita, Y. / Kimura, T.K. / Nomura, N. / Suno, R. / Morimoto, K. / Yamamoto, M. / Noda, T. / Iwata, S. / Shigematsu, H. / Kobayashi, T.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP19J12880 Japan
Japan Agency for Medical Research and Development (AMED)JP20gm0910007 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0401020 Japan
Japan Agency for Medical Research and Development (AMED)JP20ak0101103 Japan
Japan Agency for Medical Research and Development (AMED)JP19am0101115 Japan
CitationJournal: Structure / Year: 2021
Title: Cryo-EM Structure of the Prostaglandin E Receptor EP4 Coupled to G Protein.
Authors: Shingo Nojima / Yoko Fujita / Kanako Terakado Kimura / Norimichi Nomura / Ryoji Suno / Kazushi Morimoto / Masaki Yamamoto / Takeshi Noda / So Iwata / Hideki Shigematsu / Takuya Kobayashi /
Abstract: Prostaglandin E receptor EP4, a class A G protein-coupled receptor (GPCR), is a common drug target in various disorders, such as acute decompensated heart failure and ulcerative colitis. Here, we ...Prostaglandin E receptor EP4, a class A G protein-coupled receptor (GPCR), is a common drug target in various disorders, such as acute decompensated heart failure and ulcerative colitis. Here, we report the cryoelectron microscopy (cryo-EM) structure of the EP4-heterotrimeric G protein (Gs) complex with the endogenous ligand at a global resolution of 3.3 Å. In this structure, compared with that in the inactive EP4 structure, the sixth transmembrane domain is shifted outward on the intracellular side, although the shift is smaller than that in other class A GPCRs bound to Gs. Instead, the C-terminal helix of Gs is inserted toward TM2 of EP4, and the conserved C-terminal hook structure formsthe extended state. These structural features are formed by the conserved residues in prostanoid receptors (Phe54 and Trp327). These findings may be important for the thorough understanding of the G protein-binding mechanism of EP4 and other prostanoid receptors.
History
DepositionOct 5, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 2.0Dec 2, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / em_software / entity / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / struct_conf / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] ..._atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_seq_id / _em_software.category / _em_software.fitting_id / _em_software.imaging_id / _em_software.name / _em_software.version / _entity.details / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id
Description: Atoms with unrealistic or zero occupancies
Details: We removed H atoms from the previous coordinates because the density of them were not observed in the EM map. We also adjusted the residue numbers of some chains for the sequence of the wild ...Details: We removed H atoms from the previous coordinates because the density of them were not observed in the EM map. We also adjusted the residue numbers of some chains for the sequence of the wild type so that the readers of our paper will refer the coordinate file easily.
Provider: author / Type: Coordinate replacement
Revision 2.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 2.2Mar 17, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 2.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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  • Deposited structure unit
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  • EMDB-30608
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Assembly

Deposited unit
A: Prostaglandin E2 receptor EP4 subtype,Prostaglandin E2 receptor EP4 subtype
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
C: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
D: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
E: nanobody Nb35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,5906
Polymers126,2385
Non-polymers3521
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area10500 Å2
ΔGint-73 kcal/mol
Surface area42730 Å2

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Components

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Guanine nucleotide-binding protein ... , 3 types, 3 molecules BCD

#2: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Transducin beta chain 1


Mass: 37728.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNB1 / Plasmid: pFastBac Dual / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P62873
#3: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / G gamma-I


Mass: 7861.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNG2 / Plasmid: pFastBac Dual / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P59768
#4: Protein Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short / Adenylate cyclase-stimulating G alpha protein


Mass: 29014.750 Da / Num. of mol.: 1
Mutation: 65 to 203, 255 to 264 deletion G49D, E50N, L63Y, A249D, S252D, I372A and V375I
Source method: isolated from a genetically manipulated source
Details: residues from 65 to 203, residues from 255 to 264 were deleted
Source: (gene. exp.) Homo sapiens (human) / Gene: GNAS, GNAS1, GSP / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P63092

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Protein / Antibody / Non-polymers , 3 types, 3 molecules AE

#1: Protein Prostaglandin E2 receptor EP4 subtype,Prostaglandin E2 receptor EP4 subtype / PGE2 receptor EP4 subtype / Prostanoid EP4 receptor


Mass: 36953.453 Da / Num. of mol.: 1 / Mutation: N7Q, N177Q, 218-259 deletion
Source method: isolated from a genetically manipulated source
Details: residues from 218 to 259 were deleted / Source: (gene. exp.) Homo sapiens (human) / Gene: PTGER4, PTGER2 / Plasmid: pFastBac1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P35408
#5: Antibody nanobody Nb35


Mass: 14680.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The C-terminal "ENLYFQ" of sample sequence is a cleavaged TEV protease recognition sequence.
Source: (gene. exp.) Lama glama (llama) / Plasmid: pNY326 / Production host: Brevibacillus choshinensis (bacteria)
#6: Chemical ChemComp-P2E / (Z)-7-[(1R,2R,3R)-3-hydroxy-2-[(E,3S)-3-hydroxyoct-1-enyl]-5-oxo-cyclopentyl]hept-5-enoic acid / Prostaglandin E2


Mass: 352.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H32O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1PGE2-EP4-Gs-Gbeta1-Ggamma2-Nb35 complexCOMPLEX#1-#50MULTIPLE SOURCES
2Prostaglandin E2 receptor EP4 subtype,Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1,Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2COMPLEX#1-#31RECOMBINANT
3Guanine nucleotide-binding protein G(s) subunit alpha isoforms shortCOMPLEX#41RECOMBINANT
4nanobody Nb35COMPLEX#51RECOMBINANT
Molecular weightValue: 0.12 MDa / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Homo sapiens (human)9606
34Lama glama (llama)9844
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Spodoptera frugiperda (fall armyworm)7108
23Escherichia coli BL21(DE3) (bacteria)469008
34Brevibacillus choshinensis (bacteria)54911
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMHEPES1
2100 mMsodium chlorideNaCl1
30.00075 %lauryl maltose neopentyl glycol1
40.00025 %GDN1
50.000125 %cholesteryl hemisuccinate1
60.01 mMprostaglandin E 21
SpecimenConc.: 8.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 10 mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K / Details: Blot Force 10, Blot Time 3.5 sec, 3 microL apply

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Residual tilt: 0.01 mradians
Image recordingAverage exposure time: 1.83 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5743
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 25 eV
Image scansSampling size: 5 µm / Width: 4092 / Height: 5760

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Processing

EM software
IDNameVersionCategoryDetails
2SerialEM3.8.0BETAimage acquisitionOriginal script by Rado Danev
4CTFFIND4CTF correction
7Coot0.8.9.2model fitting
9PHENIX1.18-3845model refinement
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 2796263
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 178217 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-ID
15YWY

5ywy

A5YWY1
26GDG

6gdg

B6GDG2
36GDG

6gdg

C6GDG2
46GDG

6gdg

D6GDG2
56GDG

6gdg

E6GDG2

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