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- EMDB-24733: Oxytocin receptor (OTR) bound to oxytocin in complex with a heter... -

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Basic information

Entry
Database: EMDB / ID: EMD-24733
TitleOxytocin receptor (OTR) bound to oxytocin in complex with a heterotrimeric Gq protein
Map dataCombined map from local refinements
Sample
  • Complex: Oxytocin receptor signaling complex with oxytocin and miniGq and an scFv
    • Complex: Oxytocin
      • Protein or peptide: Oxytocin
    • Complex: Oxytocin receptor
      • Protein or peptide: Oxytocin receptor
    • Complex: miniGq
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2, Guanine nucleotide-binding protein G(i) subunit alpha-2,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Complex: scFv16
      • Protein or peptide: scFv16
  • Ligand: MAGNESIUM ION
KeywordsHORMONE / GPCR COMPLEX / TRANSMEMBRANE RECEPTOR / OXYTOCIN RECEPTOR / OTR / OT / OXTR / G PROTEIN / OXYTOCIN / VASOTOCIN / MEMBRANE PROTEIN / MEMBRANE PROTEIN-NEUROPEPTIDE complex
Function / homology
Function and homology information


oxytocin receptor activity / positive regulation of hindgut contraction / maternal aggressive behavior / response to anoxia / oxytocin receptor binding / neurohypophyseal hormone activity / V1A vasopressin receptor binding / Vasopressin-like receptors / response to prostaglandin E / 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 / neurohypophyseal hormone activity / V1A vasopressin receptor binding / Vasopressin-like receptors / response to prostaglandin E / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / 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 / positive regulation of blood pressure / neuropeptide hormone activity / maternal behavior / positive regulation of ossification / digestive tract development / positive regulation of synapse assembly / positive regulation of female receptivity / response to food / eating behavior / male mating behavior / suckling behavior / microvillus / peptide hormone binding / social behavior / estrous cycle / positive regulation of synaptic transmission / response to retinoic acid / response to electrical stimulus / response to glucocorticoid / cellular response to hormone stimulus / positive regulation of vasoconstriction / muscle contraction / response to cAMP / lactation / negative regulation of blood pressure / ERK1 and ERK2 cascade / response to amphetamine / regulation of heart rate / positive regulation of synaptic transmission, glutamatergic / secretory granule / response to cytokine / response to activity / response to progesterone / positive regulation of synaptic transmission, GABAergic / female pregnancy / response to cocaine / adherens junction / peptide binding / 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 / response to peptide hormone / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / ADP signalling through P2Y purinoceptor 12 / Sensory perception of sweet, bitter, and umami (glutamate) taste / 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 / cellular response to catecholamine stimulus / ADORA2B mediated anti-inflammatory cytokines production / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / 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 / Inactivation, recovery and regulation of the phototransduction cascade / heterotrimeric G-protein complex / G alpha (12/13) signalling events / extracellular vesicle / signaling receptor complex adaptor activity
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 / Guanine nucleotide-binding protein, beta subunit ...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 / 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
Similarity search - Domain/homology
Oxytocin-neurophysin 1 / Oxytocin receptor / 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: 2.9 Å
AuthorsMeyerowitz JG / Panova O / Skiniotis G
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32-GM089626 United States
CitationJournal: Nat Struct Mol Biol / Year: 2022
Title: The oxytocin signaling complex reveals a molecular switch for cation dependence.
Authors: Justin G Meyerowitz / Michael J Robertson / Ximena Barros-Álvarez / Ouliana Panova / Robert M Nwokonko / Yang Gao / Georgios Skiniotis /
Abstract: Oxytocin (OT) and vasopressin (AVP) are conserved peptide signaling hormones that are critical for diverse processes including osmotic homeostasis, reproduction, lactation and social interaction. OT ...Oxytocin (OT) and vasopressin (AVP) are conserved peptide signaling hormones that are critical for diverse processes including osmotic homeostasis, reproduction, lactation and social interaction. OT acts through the oxytocin receptor (OTR), a magnesium-dependent G protein-coupled receptor that is a therapeutic target for treatment of postpartum hemorrhage, dysfunctional labor and autism. However, the molecular mechanisms that underlie OTR activation by OT and the dependence on magnesium remain unknown. Here we present the wild-type active-state structure of human OTR bound to OT and miniG determined by cryo-EM. The structure reveals a unique activation mechanism adopted by OTR involving both the formation of a Mg coordination complex between OT and the receptor, and disruption of transmembrane helix 7 (TM7) by OT. Our functional assays demonstrate the role of TM7 disruption and provide the mechanism of full agonism by OT and partial agonism by OT analogs. Furthermore, we find that the identity of a single cation-coordinating residue across vasopressin family receptors determines whether the receptor is cation-dependent. Collectively, these results demonstrate how the Mg-dependent OTR is activated by OT, provide essential information for structure-based drug discovery efforts and shed light on the molecular determinants of cation dependence of vasopressin family receptors throughout the animal kingdom.
History
DepositionAug 24, 2021-
Header (metadata) releaseMar 9, 2022-
Map releaseMar 9, 2022-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
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  • Surface view colored by height
  • Surface level: 1
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  • Surface view with fitted model
  • Atomic models: PDB-7ryc
  • Surface level: 1
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24733.png

Downloads & links

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Map

FileDownload / File: emd_24733.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCombined map from local refinements
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 272.672 Å		0.85 Å/pix.
x 320 pix.
= 272.672 Å		0.85 Å/pix.
x 320 pix.
= 272.672 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8521 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-0.0001307 - 13.390756
Average (Standard dev.)0.008102445 (±0.12830263)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.672 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.85210.85210.8521
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z272.672272.672272.672
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.00013.3910.008

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Supplemental data

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Additional map: Local refinement of TMs with deepEMhancer sharpening

Fileemd_24733_additional_1.map
AnnotationLocal refinement of TMs with deepEMhancer sharpening
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local refinement of G protein

Fileemd_24733_additional_2.map
AnnotationLocal refinement of G protein
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Global non-uniform refinement

Fileemd_24733_additional_3.map
AnnotationGlobal non-uniform refinement
Projections & Slices
AxesZYX

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Sample components

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Entire : Oxytocin receptor signaling complex with oxytocin and miniGq and ...

EntireName: Oxytocin receptor signaling complex with oxytocin and miniGq and an scFv
Components
  • Complex: Oxytocin receptor signaling complex with oxytocin and miniGq and an scFv
    • Complex: Oxytocin
      • Protein or peptide: Oxytocin
    • Complex: Oxytocin receptor
      • Protein or peptide: Oxytocin receptor
    • Complex: miniGq
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2, Guanine nucleotide-binding protein G(i) subunit alpha-2,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Complex: scFv16
      • Protein or peptide: scFv16
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Oxytocin receptor signaling complex with oxytocin and miniGq and ...

SupramoleculeName: Oxytocin receptor signaling complex with oxytocin and miniGq and an scFv
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5

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Supramolecule #2: Oxytocin

SupramoleculeName: Oxytocin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human) / Synthetically produced: Yes

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Supramolecule #3: Oxytocin receptor

SupramoleculeName: Oxytocin receptor / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: miniGq

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

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Supramolecule #5: scFv16

SupramoleculeName: scFv16 / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Oxytocin

MacromoleculeName: Oxytocin / type: protein_or_peptide / ID: 1 / Details: C-C cyclized nonapeptide / 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 #2: Oxytocin receptor

MacromoleculeName: Oxytocin receptor / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.627074 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKTIIALSYI FCLVFADYKD DDDAMGQPGN GSAFLLAPNR SHAPDHDVEN LYFQGMEGAL AANWSAEAAN ASAAPPGAEG NRTAGPPRR NEALARVEVA VLCLILLLAL SGNACVLLAL RTTRQKHSRL FFFMKHLSIA DLVVAVFQVL PQLLWDITFR F YGPDLLCR ...String:
MKTIIALSYI FCLVFADYKD DDDAMGQPGN GSAFLLAPNR SHAPDHDVEN LYFQGMEGAL AANWSAEAAN ASAAPPGAEG NRTAGPPRR NEALARVEVA VLCLILLLAL SGNACVLLAL RTTRQKHSRL FFFMKHLSIA DLVVAVFQVL PQLLWDITFR F YGPDLLCR LVKYLQVVGM FASTYLLLLM SLDRCLAICQ PLRSLRRRTD RLAVLATWLG CLVASAPQVH IFSLREVADG VF DCWAVFI QPWGPKAYIT WITLAVYIVP VIVLAACYGL ISFKIWQNLR LKTAAAAAAE APEGAAAGDG GRVALARVSS VKL ISKAKI RTVKMTFIIV LAFIVCWTPF FFVQMWSVWD ANAPKEASAF IIVMLLASLN SCCNPWIYML FTGHLFHELV QRFL CCSAS YLKGRRLGET SASKKSNSSS FVLSHRSSSQ RSCSQPSTAL EVLFQ

UniProtKB: Oxytocin receptor

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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, Guanine nucleotide-binding protein G(i) subunit alpha-2,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.573531 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI LGSAGSAGSA MGSTVSAED KAAAERSKMI DKNLREDGEK ARRTLRLLLL GADNSGKSTI VKQMRILHGG SGGSGGTSGI FETKFQVDKV N FHMFDVGG ...String:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI LGSAGSAGSA MGSTVSAED KAAAERSKMI DKNLREDGEK ARRTLRLLLL GADNSGKSTI VKQMRILHGG SGGSGGTSGI FETKFQVDKV N FHMFDVGG QRDERRKWIQ CFNDVTAIIF VVDSSDYNRL QEALNDFKSI WNNRWLRTIS VILFLNKQDL LAEKVLAGKS KI EDYFPEF ARYTTPEDAT PEPGEDPRVT RAKYFIRKEF VDISTASGDG RHICYPHFTC AVDTENARRI FNDCKDIILQ MNL REYNLV

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Macromolecule #4: 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: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.728152 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GPGSSGSELD QLRQEAEQLK NQIRDARKAC ADATLSQITN NIDPVGRIQM RTRRTLRGHL AKIYAMHWGT DSRLLVSASQ DGKLIIWDS YTTNKVHAIP LRSSWVMTCA YAPSGNYVAC GGLDNICSIY NLKTREGNVR VSRELAGHTG YLSCCRFLDD N QIVTSSGD ...String:
GPGSSGSELD QLRQEAEQLK NQIRDARKAC ADATLSQITN NIDPVGRIQM RTRRTLRGHL AKIYAMHWGT DSRLLVSASQ DGKLIIWDS YTTNKVHAIP LRSSWVMTCA YAPSGNYVAC GGLDNICSIY NLKTREGNVR VSRELAGHTG YLSCCRFLDD N QIVTSSGD TTCALWDIET GQQTTTFTGH TGDVMSLSLA PDTRLFVSGA CDASAKLWDV REGMCRQTFT GHESDINAIC FF PNGNAFA TGSDDATCRL FDLRADQELM TYSHDNIICG ITSVSFSKSG RLLLAGYDDF NCNVWDALKA DRAGVLAGHD NRV SCLGVT DDGMAVATGS WDSFLKIWN

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

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Macromolecule #5: scFv16

MacromoleculeName: scFv16 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 27.720795 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 KAAAASSEDL YFQ

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 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: 7.4
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 40 / Average exposure time: 2.497 sec. / Average electron dose: 54.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -0.0018000000000000002 µm / Nominal defocus min: -0.0008 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initio reconstruction
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 423703
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL / Overall B value: 69.03
Output model

PDB-7ryc:
Oxytocin receptor (OTR) bound to oxytocin in complex with a heterotrimeric Gq protein

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