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Entry
Database: EMDB / ID: EMD-38185
TitleIdentification, structure and agonist design of an androgen membrane receptor
Map data
Sample
  • Complex: Complex of GPR133 with agonist and G protein trimer.
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Protein or peptide: Adhesion G-protein coupled receptor D1
    • Protein or peptide: scFv16
    • Protein or peptide: Gs protein alpha subunit
  • Ligand: (5S,8R,9S,10S,13S,14S,17S)-17-hydroxy-1,10,13-trimethyl-4,5,6,7,8,9,11,12,14,15,16,17-dodecahydrocyclopenta[a]phenanthren-3-one
KeywordsGPCR-G protein complex / MEMBRANE PROTEIN
Function / homology
Function and homology information


G-protein activation / Activation of the phototransduction cascade / Glucagon-type ligand receptors / Thromboxane signalling through TP receptor / Sensory perception of sweet, bitter, and umami (glutamate) taste / G beta:gamma signalling through PI3Kgamma / G beta:gamma signalling through CDC42 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits ...G-protein activation / Activation of the phototransduction cascade / Glucagon-type ligand receptors / Thromboxane signalling through TP receptor / Sensory perception of sweet, bitter, and umami (glutamate) taste / G beta:gamma signalling through PI3Kgamma / G beta:gamma signalling through CDC42 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Ca2+ pathway / G alpha (z) signalling events / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (q) signalling events / G alpha (i) signalling events / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / ADP signalling through P2Y purinoceptor 1 / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through CDC42 / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G alpha (12/13) signalling events / Glucagon-type ligand receptors / G beta:gamma signalling through BTK / Thrombin signalling through proteinase activated receptors (PARs) / ADP signalling through P2Y purinoceptor 12 / Adrenaline,noradrenaline inhibits insulin secretion / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Ca2+ pathway / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (z) signalling events / Extra-nuclear estrogen signaling / G alpha (s) signalling events / photoreceptor outer segment membrane / G alpha (q) signalling events / G alpha (i) signalling events / spectrin binding / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Vasopressin regulates renal water homeostasis via Aquaporins / alkylglycerophosphoethanolamine phosphodiesterase activity / photoreceptor outer segment / photoreceptor inner segment / cardiac muscle cell apoptotic process / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cellular response to catecholamine stimulus / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / sensory perception of taste / signaling receptor complex adaptor activity / cell body / GTPase binding / retina development in camera-type eye / positive regulation of cytosolic calcium ion concentration / phospholipase C-activating G protein-coupled receptor signaling pathway / cellular response to hypoxia / cell population proliferation / cell surface receptor signaling pathway / nuclear speck / G protein-coupled receptor signaling pathway / GTPase activity / dendrite / synapse / protein-containing complex binding / nucleoplasm / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Concanavalin A-like lectin/glucanases superfamily / Pentraxin-related / Pentraxin (PTX) domain profile. / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site ...Concanavalin A-like lectin/glucanases superfamily / Pentraxin-related / Pentraxin (PTX) domain profile. / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / 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 / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / Concanavalin A-like lectin/glucanase domain superfamily / 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. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
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-2 / Adhesion G-protein coupled receptor D1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat) / Bos taurus (domestic cattle) / synthetic construct (others) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsPing YQ / Yang Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nature / Year: 2022
Title: Structural basis for the tethered peptide activation of adhesion GPCRs.
Authors: Yu-Qi Ping / Peng Xiao / Fan Yang / Ru-Jia Zhao / Sheng-Chao Guo / Xu Yan / Xiang Wu / Chao Zhang / Yan Lu / Fenghui Zhao / Fulai Zhou / Yue-Tong Xi / Wanchao Yin / Feng-Zhen Liu / Dong-Fang ...Authors: Yu-Qi Ping / Peng Xiao / Fan Yang / Ru-Jia Zhao / Sheng-Chao Guo / Xu Yan / Xiang Wu / Chao Zhang / Yan Lu / Fenghui Zhao / Fulai Zhou / Yue-Tong Xi / Wanchao Yin / Feng-Zhen Liu / Dong-Fang He / Dao-Lai Zhang / Zhong-Liang Zhu / Yi Jiang / Lutao Du / Shi-Qing Feng / Torsten Schöneberg / Ines Liebscher / H Eric Xu / Jin-Peng Sun /
Abstract: Adhesion G-protein-coupled receptors (aGPCRs) are important for organogenesis, neurodevelopment, reproduction and other processes. Many aGPCRs are activated by a conserved internal (tethered) agonist ...Adhesion G-protein-coupled receptors (aGPCRs) are important for organogenesis, neurodevelopment, reproduction and other processes. Many aGPCRs are activated by a conserved internal (tethered) agonist sequence known as the Stachel sequence. Here, we report the cryogenic electron microscopy (cryo-EM) structures of two aGPCRs in complex with G: GPR133 and GPR114. The structures indicate that the Stachel sequences of both receptors assume an α-helical-bulge-β-sheet structure and insert into a binding site formed by the transmembrane domain (TMD). A hydrophobic interaction motif (HIM) within the Stachel sequence mediates most of the intramolecular interactions with the TMD. Combined with the cryo-EM structures, biochemical characterization of the HIM motif provides insight into the cross-reactivity and selectivity of the Stachel sequences. Two interconnected mechanisms, the sensing of Stachel sequences by the conserved 'toggle switch' W and the constitution of a hydrogen-bond network formed by Q/Y and the P/VφφG motif (φ indicates a hydrophobic residue), are important in Stachel sequence-mediated receptor activation and G coupling. Notably, this network stabilizes kink formation in TM helices 6 and 7 (TM6 and TM7, respectively). A common G-binding interface is observed between the two aGPCRs, and GPR114 has an extended TM7 that forms unique interactions with G. Our structures reveal the detailed mechanisms of aGPCR activation by Stachel sequences and their G coupling.
History
DepositionDec 1, 2023-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38185.png

Downloads & links

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Map

FileDownload / File: emd_38185.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 250 pix.
= 232.5 Å		0.93 Å/pix.
x 250 pix.
= 232.5 Å		0.93 Å/pix.
x 250 pix.
= 232.5 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.0017242276 - 1.8439565
Average (Standard dev.)0.0014016324 (±0.026529564)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 232.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_38185_msk_1.map
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Half map: #2

Fileemd_38185_half_map_1.map
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Half map: #1

Fileemd_38185_half_map_2.map
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Sample components

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Entire : Complex of GPR133 with agonist and G protein trimer.

EntireName: Complex of GPR133 with agonist and G protein trimer.
Components
  • Complex: Complex of GPR133 with agonist and G protein trimer.
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Protein or peptide: Adhesion G-protein coupled receptor D1
    • Protein or peptide: scFv16
    • Protein or peptide: Gs protein alpha subunit
  • Ligand: (5S,8R,9S,10S,13S,14S,17S)-17-hydroxy-1,10,13-trimethyl-4,5,6,7,8,9,11,12,14,15,16,17-dodecahydrocyclopenta[a]phenanthren-3-one

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Supramolecule #1: Complex of GPR133 with agonist and G protein trimer.

SupramoleculeName: Complex of GPR133 with agonist and G protein trimer. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2, #5, #3-#4
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 37.784301 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GSLLQSELDQ LRQEAEQLKN QIRDARKACA DATLSQITNN IDPVGRIQMR TRRTLRGHLA KIYAMHWGTD SRLLVSASQD GKLIIWDSY TTNKVHAIPL RSSWVMTCAY APSGNYVACG GLDNICSIYN LKTREGNVRV SRELAGHTGY LSCCRFLDDN Q IVTSSGDT ...String:
GSLLQSELDQ LRQEAEQLKN QIRDARKACA DATLSQITNN IDPVGRIQMR TRRTLRGHLA KIYAMHWGTD SRLLVSASQD GKLIIWDSY TTNKVHAIPL RSSWVMTCAY APSGNYVACG GLDNICSIYN LKTREGNVRV SRELAGHTGY LSCCRFLDDN Q IVTSSGDT TCALWDIETG QQTTTFTGHT GDVMSLSLAP DTRLFVSGAC DASAKLWDVR EGMCRQTFTG HESDINAICF FP NGNAFAT GSDDATCRLF DLRADQELMT YSHDNIICGI TSVSFSKSGR LLLAGYDDFN CNVWDALKAD RAGVLAGHDN RVS CLGVTD DGMAVATGSW DSFLKIWN

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

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Macromolecule #2: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 7.861143 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

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Macromolecule #3: scFv16

MacromoleculeName: scFv16 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 28.781988 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SAGGGGSGGG GSGGGGSSDI VMTQATSSVP VTPGESVSIS C RSSKSLLH ...String:
MVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SAGGGGSGGG GSGGGGSSDI VMTQATSSVP VTPGESVSIS C RSSKSLLH SNGNTYLYWF LQRPGQSPQL LIYRMSNLAS GVPDRFSGSG SGTAFTLTIS RLEAEDVGVY YCMQHLEYPL TF GAGTKLE LLEENLYFQG ASHHHHHHHH

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Macromolecule #4: Gs protein alpha subunit

MacromoleculeName: Gs protein alpha subunit / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 41.879465 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGCTLSAEDK AAVERSKMIE KQLQKDKQVY RATHRLLLLG ADNSGKSTIV KQMRIYHVNG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI ...String:
MGCTLSAEDK AAVERSKMIE KQLQKDKQVY RATHRLLLLG ADNSGKSTIV KQMRIYHVNG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI PTQQDVLRTR VKTSGIFETK FQVDKVNFHM FDVGAQRDER RKWIQCFNDV TAIIFVVDSS DYNRLQEALN DF KSIWNNR WLRTISVILF LNKQDLLAEK VLAGKSKIED YFPEFARYTT PEDATPEPGE DPRVTRAKYF IRDEFLRIST ASG DGRHYC YPHFTCSVDT ENARRIFNDC RDIIQRMHLR QYELL

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Macromolecule #5: Adhesion G-protein coupled receptor D1

MacromoleculeName: Adhesion G-protein coupled receptor D1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 65.688828 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: HPIITNLTEE RKTFQSPGVI LSYLQNVSLS LPSKSLSEQT ALNLTKTFLK AVGEILLLPG WIALSEDSAV VLSLIDTIDT VMGHVSSNL HGSTPQVTVE GSSAMAEFSV AKILPKTVNS SHYRFPAHGQ SFIQIPHEAF HRHAWSTVVG LLYHSMHYYL N NIWPAHTK ...String:
HPIITNLTEE RKTFQSPGVI LSYLQNVSLS LPSKSLSEQT ALNLTKTFLK AVGEILLLPG WIALSEDSAV VLSLIDTIDT VMGHVSSNL HGSTPQVTVE GSSAMAEFSV AKILPKTVNS SHYRFPAHGQ SFIQIPHEAF HRHAWSTVVG LLYHSMHYYL N NIWPAHTK IAEAMHHQDC LLFATSHLIS LEVSPPPTLS QNLSGSPLIT VHLKHRLTRK QHSEATNSSN RVFVYCAFLD FS SGEGVWS NHGCALTRGN LTYSVCRCTH LTNFAILMQV VPLELARGHQ VALSSISYVG CSLSVLCLVA TLVTFAVLSS VST IRNQRY HIHANLSFAV LVAQVLLLIS FRLEPGTTPC QVMAVLLHYF FLSAFAWMLV EGLHLYSMVI KVFGSEDSKH RYYY GMGWG FPLLICIISL SFAMDSYGTS NNCWLSLASG AIWAFVAPAL FVIVVNIGIL IAVTRVISQI SADNYKIHGD PSAFK LTAK AVAVLLPILG TSWVFGVLAV NGCAVVFQYM FATLNSLQGL FIFLFHCLLN SEVRAAFKHK TKVWSLTSSS ARTSNA KPF HSDLMNGTRP GMASTKLSPW DKSSHSAHRV DLSAV

UniProtKB: Adhesion G-protein coupled receptor D1

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Macromolecule #6: (5S,8R,9S,10S,13S,14S,17S)-17-hydroxy-1,10,13-trimethyl-4,5,6,7,8...

MacromoleculeName: (5S,8R,9S,10S,13S,14S,17S)-17-hydroxy-1,10,13-trimethyl-4,5,6,7,8,9,11,12,14,15,16,17-dodecahydrocyclopenta[a]phenanthren-3-one
type: ligand / ID: 6 / Number of copies: 1 / Formula: A1LU1
Molecular weightTheoretical: 302.451 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 180186
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model
Output model

PDB-8x9u:
Identification, structure and agonist design of an androgen membrane receptor

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