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- EMDB-14180: Human Oxytocin receptor (OTR) oxytocin Gq chimera (mGoqi) complex -

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Basic information

Entry
Database: EMDB / ID: EMD-14180
TitleHuman Oxytocin receptor (OTR) oxytocin Gq chimera (mGoqi) complex
Map dataprimary map
Sample
  • Complex: OTR in complex with Oxytocin, heterotrimeric mini-Gq chimera (Goqi) and scFv16
    • Complex: Heterotrimeric mini-Gq chimera (Goqi) and Oxytocin receptor
      • Protein or peptide: Guanine nucleotide-binding protein G(o) subunit alpha,cDNA FLJ31446 fis, clone NT2NE2000909, highly similar to Guanine nucleotide-binding protein G(o) subunit alpha 1
      • 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: Oxytocin receptor
    • Complex: Oxytocin
      • Protein or peptide: Oxytocin
    • Complex: Antibody fragment scFv16
      • Protein or peptide: Antibody fragment scFv16
KeywordsGPCR / OTR / G protein / OT / scFv16 / mGoqi / oxytocin / membrane protein / SIGNALING PROTEIN
Function / homology
Function and homology information


oxytocin receptor activity / positive regulation of hindgut contraction / maternal aggressive behavior / response to anoxia / oxytocin receptor binding / guanyl nucleotide binding / neurohypophyseal hormone activity / V1A vasopressin receptor binding / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin ...oxytocin receptor activity / positive regulation of hindgut contraction / maternal aggressive behavior / response to anoxia / oxytocin receptor binding / guanyl nucleotide binding / neurohypophyseal hormone activity / V1A vasopressin receptor binding / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / response to prostaglandin E / positive regulation of uterine smooth muscle contraction / maternal process involved in parturition / positive regulation of penile erection / positive regulation of norepinephrine secretion / negative regulation of urine volume / sperm ejaculation / telencephalon development / drinking behavior / grooming behavior / response to sucrose / positive regulation of prostaglandin secretion / response to ether / mu-type opioid receptor binding / corticotropin-releasing hormone receptor 1 binding / positive regulation of blood pressure / neuropeptide hormone activity / maternal behavior / digestive tract development / positive regulation of ossification / vesicle docking involved in exocytosis / positive regulation of synapse assembly / positive regulation of female receptivity / response to food / G protein-coupled dopamine receptor signaling pathway / eating behavior / regulation of heart contraction / male mating behavior / suckling behavior / peptide hormone binding / microvillus / social behavior / estrous cycle / positive regulation of synaptic transmission / negative regulation of insulin secretion / response to electrical stimulus / G protein-coupled serotonin receptor binding / response to retinoic acid / response to glucocorticoid / cellular response to hormone stimulus / positive regulation of vasoconstriction / muscle contraction / response to cAMP / negative regulation of blood pressure / lactation / response to amphetamine / ERK1 and ERK2 cascade / regulation of heart rate / positive regulation of synaptic transmission, glutamatergic / response to cytokine / secretory granule / response to cocaine / response to activity / response to progesterone / positive regulation of synaptic transmission, GABAergic / female pregnancy / locomotory behavior / adherens junction / peptide binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Olfactory Signaling Pathway / Activation of the phototransduction cascade / terminal bouton / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / G-protein activation / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / memory / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / response to peptide hormone / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / photoreceptor disc membrane / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / cellular response to catecholamine stimulus / sensory perception of taste
Similarity search - Function
Oxytocin receptor / Neurohypophysial hormone / Neurohypophysial hormone, conserved site / Neurohypophysial hormone domain superfamily / Neurohypophysial hormones, C-terminal Domain / Neurohypophysial hormones, N-terminal Domain / Neurohypophysial hormones signature. / Neurohypophysial hormones / Vasopressin receptor / G-protein alpha subunit, group I ...Oxytocin receptor / Neurohypophysial hormone / Neurohypophysial hormone, conserved site / Neurohypophysial hormone domain superfamily / Neurohypophysial hormones, C-terminal Domain / Neurohypophysial hormones, N-terminal Domain / Neurohypophysial hormones signature. / Neurohypophysial hormones / Vasopressin receptor / G-protein alpha subunit, group I / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / 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 / 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. / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Guanine nucleotide-binding protein G(o) subunit alpha / Guanine nucleotide-binding protein G(o) subunit alpha / Oxytocin-neurophysin 1 / Guanine nucleotide-binding protein G(o) subunit alpha / Oxytocin receptor / 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
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsWaltenspuhl Y / Ehrenmann J
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_182334 Switzerland
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis for the activation and ligand recognition of the human oxytocin receptor.
Authors: Yann Waltenspühl / Janosch Ehrenmann / Santiago Vacca / Cristian Thom / Ohad Medalia / Andreas Plückthun /
Abstract: The small cyclic neuropeptide hormone oxytocin (OT) and its cognate receptor play a central role in the regulation of social behaviour and sexual reproduction. Here we report the single-particle cryo- ...The small cyclic neuropeptide hormone oxytocin (OT) and its cognate receptor play a central role in the regulation of social behaviour and sexual reproduction. Here we report the single-particle cryo-electron microscopy structure of the active oxytocin receptor (OTR) in complex with its cognate ligand oxytocin. Our structure provides high-resolution insights into the OT binding mode, the OTR activation mechanism as well as the subtype specificity within the oxytocin/vasopressin receptor family.
History
DepositionJan 21, 2022-
Header (metadata) releaseAug 10, 2022-
Map releaseAug 10, 2022-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14180.png

Downloads & links

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Map

FileDownload / File: emd_14180.map.gz / Format: CCP4 / Size: 266.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprimary map
Projections & slices

Image control

Size
Brightness
Contrast
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AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 412 pix.
= 268.212 Å		0.65 Å/pix.
x 412 pix.
= 268.212 Å		0.65 Å/pix.
x 412 pix.
= 268.212 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.651 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.169
Minimum - Maximum-0.6546487 - 1.3876247
Average (Standard dev.)-0.000024180672 (±0.025879454)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions412412412
Spacing412412412
CellA=B=C: 268.212 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: raw map

Fileemd_14180_additional_1.map
Annotationraw map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : OTR in complex with Oxytocin, heterotrimeric mini-Gq chimera (Goq...

EntireName: OTR in complex with Oxytocin, heterotrimeric mini-Gq chimera (Goqi) and scFv16
Components
  • Complex: OTR in complex with Oxytocin, heterotrimeric mini-Gq chimera (Goqi) and scFv16
    • Complex: Heterotrimeric mini-Gq chimera (Goqi) and Oxytocin receptor
      • Protein or peptide: Guanine nucleotide-binding protein G(o) subunit alpha,cDNA FLJ31446 fis, clone NT2NE2000909, highly similar to Guanine nucleotide-binding protein G(o) subunit alpha 1
      • 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: Oxytocin receptor
    • Complex: Oxytocin
      • Protein or peptide: Oxytocin
    • Complex: Antibody fragment scFv16
      • Protein or peptide: Antibody fragment scFv16

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Supramolecule #1: OTR in complex with Oxytocin, heterotrimeric mini-Gq chimera (Goq...

SupramoleculeName: OTR in complex with Oxytocin, heterotrimeric mini-Gq chimera (Goqi) and scFv16
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Heterotrimeric mini-Gq chimera (Goqi) and Oxytocin receptor

SupramoleculeName: Heterotrimeric mini-Gq chimera (Goqi) and Oxytocin receptor
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3, #5
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Oxytocin

SupramoleculeName: Oxytocin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Antibody fragment scFv16

SupramoleculeName: Antibody fragment scFv16 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #6
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Guanine nucleotide-binding protein G(o) subunit alpha,cDNA FLJ314...

MacromoleculeName: Guanine nucleotide-binding protein G(o) subunit alpha,cDNA FLJ31446 fis, clone NT2NE2000909, highly similar to Guanine nucleotide-binding protein G(o) subunit alpha 1
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.650412 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGCTLSAEDK AAVERSKMIE KNLKEDGISA AKDVKLLLLG ADNSGKSTIV KQMKIIHGGS GGSGGTTGIV ETHFTFKNLH FRLFDVGGQ RSERKKWIHC FEDVTAIIFC VDLSDYNRMH ESLMLFDSIC NNKFFIDTSI ILFLNKKDLF GEKIKKSPLT I CFPEYTGP ...String:
MGCTLSAEDK AAVERSKMIE KNLKEDGISA AKDVKLLLLG ADNSGKSTIV KQMKIIHGGS GGSGGTTGIV ETHFTFKNLH FRLFDVGGQ RSERKKWIHC FEDVTAIIFC VDLSDYNRMH ESLMLFDSIC NNKFFIDTSI ILFLNKKDLF GEKIKKSPLT I CFPEYTGP NTYEDAAAYI QAQFESKNRS PNKEIYCHMT CATDTNNAQV IFDAVTDIIL QMNLREYNLV

UniProtKB: Guanine nucleotide-binding protein G(o) subunit alpha, Guanine nucleotide-binding protein G(o) subunit alpha, Guanine nucleotide-binding protein G(o) subunit alpha

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Macromolecule #2: 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: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.086641 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHHHH HGSSGSELDQ LRQEAEQLKN QIRDARKACA DATLSQITNN IDPVGRIQMR TRRTLRGHLA KIYAMHWGTD SRLLVSASQ DGKLIIWDSY TTNKVHAIPL RSSWVMTCAY APSGNYVACG GLDNICSIYN LKTREGNVRV SRELAGHTGY L SCCRFLDD ...String:
MHHHHHHHHH HGSSGSELDQ 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

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

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Macromolecule #3: 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: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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 #4: Oxytocin

MacromoleculeName: Oxytocin / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.008196 KDa
SequenceString:
CYIQNCPLG(NH2)

UniProtKB: Oxytocin-neurophysin 1

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Macromolecule #5: Oxytocin receptor

MacromoleculeName: Oxytocin receptor / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.777293 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEGALAANWS AEAANASAAP PGAEGNRTAG PPRRNEALAR VEVAVLCLIL LLALSGNACV LLALRTTRQK HSRLFFFMKH LSIADLVVA VFQVLPQLLW DITFRFYGPD LLCRLVKYLQ VVGMFASTYL LLLMSLDRCL AICQPLRSLR RRTYRLAVLA T WLGCLVAS ...String:
MEGALAANWS AEAANASAAP PGAEGNRTAG PPRRNEALAR VEVAVLCLIL LLALSGNACV LLALRTTRQK HSRLFFFMKH LSIADLVVA VFQVLPQLLW DITFRFYGPD LLCRLVKYLQ VVGMFASTYL LLLMSLDRCL AICQPLRSLR RRTYRLAVLA T WLGCLVAS APQVHIFSLR EVADGVFDCW AVFIQPWGPK AYITWITLAV YIVPVIVLAT CYGLISFKIW QNLRLKTAAA AA AEAPEGA AAGDGGRVAL ARVSSVKLIS KAKIRTVKMT FIIVLAFIVC WTPFFFVQMW SVWDANAPKE ASAFIIVMLL ASL NSCCNP WIYMLFTGHL FHELVQRFLC CSASYLKGRR LGK

UniProtKB: Oxytocin receptor

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Macromolecule #6: Antibody fragment scFv16

MacromoleculeName: Antibody fragment scFv16 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 26.679721 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS ...String:
DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS NGNTYLYWFL QRPGQSPQLL IYRMSNLASG VPDRFSGSGS GTAFTLTISR LEAEDVGVYY CMQHLEYPLT FG AGTKLEL KAAA

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 63.78 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 392369
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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