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- EMDB-25389: Structure of the orexin-2 receptor(OX2R) bound to TAK-925, Gi and... -

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Entry
Database: EMDB / ID: EMD-25389
TitleStructure of the orexin-2 receptor(OX2R) bound to TAK-925, Gi and scFv16
Map dataOrexin-2 receptor (OX2R) bound to TAK-925, Gi and scFv16
Sample
  • Complex: Human OX2R in complex with Gai/Gb/Gg-scFv16.
    • Complex: Orexin receptor type 2Hypocretin (orexin) receptor 2
      • Protein or peptide: Orexin receptor type 2Hypocretin (orexin) receptor 2
    • Complex: Guanine nucleotide-binding protein G(i) subunit alpha-1
      • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1
    • Complex: 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
      • 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
    • Complex: scFv-16Single-chain variable fragment
      • Protein or peptide: scFv-16Single-chain variable fragment
  • Ligand: OLEIC ACID
  • Ligand: methyl (2R,3S)-3-[(methanesulfonyl)amino]-2-({[(1s,4S)-4-phenylcyclohexyl]oxy}methyl)piperidine-1-carboxylate
Function / homology
Function and homology information


regulation of circadian sleep/wake cycle, wakefulness / circadian sleep/wake cycle process / orexin receptor activity / Orexin and neuropeptides FF and QRFP bind to their respective receptors / neuropeptide receptor activity / Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Activation of the phototransduction cascade / locomotion ...regulation of circadian sleep/wake cycle, wakefulness / circadian sleep/wake cycle process / orexin receptor activity / Orexin and neuropeptides FF and QRFP bind to their respective receptors / neuropeptide receptor activity / Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Activation of the phototransduction cascade / locomotion / feeding behavior / 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 / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thrombin signalling through proteinase activated receptors (PARs) / Ca2+ pathway / G alpha (z) signalling events / Extra-nuclear estrogen signaling / G alpha (s) signalling events / G alpha (q) signalling events / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / peptide hormone binding / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / neuropeptide signaling pathway / regulation of cAMP-mediated signaling / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / regulation of mitotic spindle organization / cellular response to forskolin / cellular response to hormone stimulus / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / regulation of cytosolic calcium ion concentration / Regulation of insulin secretion / G protein-coupled receptor binding / peptide binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / ADP signalling through P2Y purinoceptor 12 / response to peptide hormone / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (z) signalling events / cellular response to catecholamine stimulus / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / sensory perception of taste / GPER1 signaling / GDP binding / G-protein beta-subunit binding / heterotrimeric G-protein complex / signaling receptor complex adaptor activity / retina development in camera-type eye / GTPase binding / phospholipase C-activating G protein-coupled receptor signaling pathway / cell cortex / midbody / G alpha (i) signalling events / chemical synaptic transmission / G alpha (s) signalling events / G alpha (q) signalling events / cell population proliferation / Extra-nuclear estrogen signaling / cell cycle / G protein-coupled receptor signaling pathway / cell division / lysosomal membrane / GTPase activity / centrosome / synapse / protein-containing complex binding / GTP binding / nucleolus / magnesium ion binding / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytoplasm
Similarity search - Function
Orexin receptor 2 / Orexin receptor type 2 / Orexin receptor family / G-protein alpha subunit, group I / Serpentine type 7TM GPCR chemoreceptor Srsx / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit ...Orexin receptor 2 / Orexin receptor type 2 / Orexin receptor family / G-protein alpha subunit, group I / Serpentine type 7TM GPCR chemoreceptor Srsx / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / G-protein, gamma subunit / G-protein gamma subunit domain profile. / GGL domain / G-protein gamma-like domain superfamily / G-protein gamma-like domain / GGL domain / G protein gamma subunit-like motifs / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Orexin receptor type 2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(i) subunit alpha-1 / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Similarity search - Component
Biological speciesHomo sapiens (human) / Bos taurus (cattle) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsMcGrath AP / Kang Y / Flinspach M
Funding support1 items
OrganizationGrant numberCountry
Other private
CitationJournal: Nat Commun / Year: 2022
Title: Molecular mechanism of the wake-promoting agent TAK-925.
Authors: Jie Yin / Yanyong Kang / Aaron P McGrath / Karen Chapman / Megan Sjodt / Eiji Kimura / Atsutoshi Okabe / Tatsuki Koike / Yuhei Miyanohana / Yuji Shimizu / Rameshu Rallabandi / Peng Lian / ...Authors: Jie Yin / Yanyong Kang / Aaron P McGrath / Karen Chapman / Megan Sjodt / Eiji Kimura / Atsutoshi Okabe / Tatsuki Koike / Yuhei Miyanohana / Yuji Shimizu / Rameshu Rallabandi / Peng Lian / Xiaochen Bai / Mack Flinspach / Jef K De Brabander / Daniel M Rosenbaum /
Abstract: The OX orexin receptor (OXR) is a highly expressed G protein-coupled receptor (GPCR) in the brain that regulates wakefulness and circadian rhythms in humans. Antagonism of OXR is a proven therapeutic ...The OX orexin receptor (OXR) is a highly expressed G protein-coupled receptor (GPCR) in the brain that regulates wakefulness and circadian rhythms in humans. Antagonism of OXR is a proven therapeutic strategy for insomnia drugs, and agonism of OXR is a potentially powerful approach for narcolepsy type 1, which is characterized by the death of orexinergic neurons. Until recently, agonism of OXR had been considered 'undruggable.' We harness cryo-electron microscopy of OXR-G protein complexes to determine how the first clinically tested OXR agonist TAK-925 can activate OXR in a highly selective manner. Two structures of TAK-925-bound OXR with either a G mimetic or G reveal that TAK-925 binds at the same site occupied by antagonists, yet interacts with the transmembrane helices to trigger activating microswitches. Our structural and mutagenesis data show that TAK-925's selectivity is mediated by subtle differences between OX and OX receptor subtypes at the orthosteric pocket. Finally, differences in the polarity of interactions at the G protein binding interfaces help to rationalize OXR's coupling selectivity for G signaling. The mechanisms of TAK-925's binding, activation, and selectivity presented herein will aid in understanding the efficacy of small molecule OXR agonists for narcolepsy and other circadian disorders.
History
DepositionNov 5, 2021-
Header (metadata) releaseMay 25, 2022-
Map releaseMay 25, 2022-
UpdateJul 6, 2022-
Current statusJul 6, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25389.png

Downloads & links

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Map

FileDownload / File: emd_25389.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOrexin-2 receptor (OX2R) bound to TAK-925, Gi and scFv16
Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-2.613397 - 4.2362494
Average (Standard dev.)0.008538726 (±0.098467626)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 249.59999 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Human OX2R in complex with Gai/Gb/Gg-scFv16.

EntireName: Human OX2R in complex with Gai/Gb/Gg-scFv16.
Components
  • Complex: Human OX2R in complex with Gai/Gb/Gg-scFv16.
    • Complex: Orexin receptor type 2Hypocretin (orexin) receptor 2
      • Protein or peptide: Orexin receptor type 2Hypocretin (orexin) receptor 2
    • Complex: Guanine nucleotide-binding protein G(i) subunit alpha-1
      • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1
    • Complex: 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
      • 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
    • Complex: scFv-16Single-chain variable fragment
      • Protein or peptide: scFv-16Single-chain variable fragment
  • Ligand: OLEIC ACID
  • Ligand: methyl (2R,3S)-3-[(methanesulfonyl)amino]-2-({[(1s,4S)-4-phenylcyclohexyl]oxy}methyl)piperidine-1-carboxylate

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Supramolecule #1: Human OX2R in complex with Gai/Gb/Gg-scFv16.

SupramoleculeName: Human OX2R in complex with Gai/Gb/Gg-scFv16. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5

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Supramolecule #2: Orexin receptor type 2

SupramoleculeName: Orexin receptor type 2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera (butterflies/moths)

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Supramolecule #3: Guanine nucleotide-binding protein G(i) subunit alpha-1

SupramoleculeName: Guanine nucleotide-binding protein G(i) subunit alpha-1
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

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Supramolecule #4: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1,...

SupramoleculeName: 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
type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Bos taurus (cattle)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

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Supramolecule #5: scFv-16

SupramoleculeName: scFv-16 / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

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Macromolecule #1: Orexin receptor type 2

MacromoleculeName: Orexin receptor type 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.733289 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString: MSGTKLEDSP PCRNWSSASE LNETQEPFLN PTDYDDEEFL RYLWREYLHP KEYEWVLIAG YIIVFVVALI GNVLVCVAVW KNHHMRTVT NYFIVNLSLA DVLVTITCLP ATLVVDITET WFFGQSLCKV IPYLQTVSVS VSVLTLSCIA LDRWYAICHP L MFKSTAKR ...String:
MSGTKLEDSP PCRNWSSASE LNETQEPFLN PTDYDDEEFL RYLWREYLHP KEYEWVLIAG YIIVFVVALI GNVLVCVAVW KNHHMRTVT NYFIVNLSLA DVLVTITCLP ATLVVDITET WFFGQSLCKV IPYLQTVSVS VSVLTLSCIA LDRWYAICHP L MFKSTAKR ARNSIVIIWI VSCIIMIPQA IVMECSTVFP GLANKTTLFT VCDERWGGEI YPKMYHICFF LVTYMAPLCL MV LAYLQIF RKLWCRQIPG TSSVVQRKWK PLQPVSQPRG PGQPTKSRMS AVAAEIKQIR ARRKTARMLM VVLLVFAICY LPI SILNVL KRVFGMFAHT EDRETVYAWF TFSHWLVYAN SAANPIIYNF LSGKFREEFK AAFSCCCLGV HHRQEDRLTR GRTS TESRK SLTTQISNFD NISKLSEQVV LTSISTLPAA NGAGPLQNW

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Macromolecule #2: Guanine nucleotide-binding protein G(i) subunit alpha-1

MacromoleculeName: Guanine nucleotide-binding protein G(i) subunit alpha-1
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.459039 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MGCTLSAEDK AAVERSKMID RNLREDGEKA AREVKLLLLG AGESGKSTIV KQMKIIHEAG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI ...String:
MGCTLSAEDK AAVERSKMID RNLREDGEKA AREVKLLLLG AGESGKSTIV KQMKIIHEAG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI PTQQDVLRTR VKTTGIVETH FTFKDLHFKM FDVGGQRDER KKWIHCFEGV TAIIFCVALS DYDLVLAEDE EM NRMHESM KLFDSICNNK WFTDTSIILF LNKKDLFEEK IKKSPLTICY PEYAGSNTYE EAAAYIQCQF EDLNKRKDTK EIY THFTCS TDTKNVQFVF DAVTDVIIKN NLKDCGLF

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Macromolecule #3: 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: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 39.151855 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MHHHHHHHHM GSLLQSELDQ LRQEAEQLKN QIRDARKACA DATLSQITNN IDPVGRIQMR TRRTLRGHLA KIYAMHWGTD SRLLVSASQ DGKLIIWDSY TTNKVHAIPL RSSWVMTCAY APSGNYVACG GLDNICSIYN LKTREGNVRV SRELAGHTGY L SCCRFLDD ...String:
MHHHHHHHHM GSLLQSELDQ LRQEAEQLKN QIRDARKACA DATLSQITNN IDPVGRIQMR TRRTLRGHLA KIYAMHWGTD SRLLVSASQ DGKLIIWDSY TTNKVHAIPL RSSWVMTCAY APSGNYVACG GLDNICSIYN LKTREGNVRV SRELAGHTGY L SCCRFLDD NQIVTSSGDT TCALWDIETG QQTTTFTGHT GDVMSLSLAP DTRLFVSGAC DASAKLWDVR EGMCRQTFTG HE SDINAIC FFPNGNAFAT GSDDATCRLF DLRADQELMT YSHDNIICGI TSVSFSKSGR LLLAGYDDFN CNVWDALKAD RAG VLAGHD NRVSCLGVTD DGMAVATGSW DSFLKIWN

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Macromolecule #4: 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: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 7.56375 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFC

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Macromolecule #5: scFv-16

MacromoleculeName: scFv-16 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 26.277299 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: VQLVESGGGL VQPGGSRKLS CSASGFAFSS FGMHWVRQAP EKGLEWVAYI SSGSGTIYYA DTVKGRFTIS RDDPKNTLFL QMTSLRSED TAMYYCVRSI YYYGSSPFDF WGQGTTLTVS AGGGGSGGGG SGGGGSADIV MTQATSSVPV TPGESVSISC R SSKSLLHS ...String:
VQLVESGGGL VQPGGSRKLS CSASGFAFSS FGMHWVRQAP EKGLEWVAYI SSGSGTIYYA DTVKGRFTIS RDDPKNTLFL QMTSLRSED TAMYYCVRSI YYYGSSPFDF WGQGTTLTVS AGGGGSGGGG SGGGGSADIV MTQATSSVPV TPGESVSISC R SSKSLLHS NGNTYLYWFL QRPGQSPQLL IYRMSNLASG VPDRFSGSGS GTAFTLTISR LEAEDVGVYY CMQHLEYPLT FG AGTKLEL

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Macromolecule #6: OLEIC ACID

MacromoleculeName: OLEIC ACID / type: ligand / ID: 6 / Number of copies: 4 / Formula: OLA
Molecular weightTheoretical: 282.461 Da
Chemical component information

ChemComp-OLA:
OLEIC ACID / Oleic acid

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Macromolecule #7: methyl (2R,3S)-3-[(methanesulfonyl)amino]-2-({[(1s,4S)-4-phenylcy...

MacromoleculeName: methyl (2R,3S)-3-[(methanesulfonyl)amino]-2-({[(1s,4S)-4-phenylcyclohexyl]oxy}methyl)piperidine-1-carboxylate
type: ligand / ID: 7 / Number of copies: 1 / Formula: A6F
Molecular weightTheoretical: 424.554 Da
Chemical component information

ChemComp-A6F:
methyl (2R,3S)-3-[(methanesulfonyl)amino]-2-({[(1s,4S)-4-phenylcyclohexyl]oxy}methyl)piperidine-1-carboxylate

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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

Concentration5 mg/mL
BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 130000
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 43.7 e/Å2
Details: Cryo-EM movie stacks were collected on a Titan Krios microscope operated at 300 kV under EFTEM mode. Nanoprobe with 1um illumination area was used. Data were recorded on a postGIF Gatan K2 ...Details: Cryo-EM movie stacks were collected on a Titan Krios microscope operated at 300 kV under EFTEM mode. Nanoprobe with 1um illumination area was used. Data were recorded on a postGIF Gatan K2 summit camera at a nominal magnification of 130,000, using super-resolution counting model. Bioquantum energy filter was operated in the zero-energy-loss mode with an energy slit width of 20 eV.
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 647261
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5ws3

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 251169
DetailsFrames 2-30 were used during dose-weighted movie frame alignment to reduce effects of beam-induced motion. Parameters of the FEI Titan Krios contrast transfer function were subsequently estimated for each micrograph. A total 647,261 particles were auto-picked using Template Picker and extracted in 220 x 220 pixels box using cryoSPARC. All particles were subject to three rounds of reference-free 2D classification. Four initial model were made using cryoSPARC based on selected particles. The final 3D refinement in cryoSPARC2 used 251,169 particles, producing a reconstruction with 3.17A nominal resolution.
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-7sqo:
Structure of the orexin-2 receptor(OX2R) bound to TAK-925, Gi and scFv16

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