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- PDB-7qvm: Human Oxytocin receptor (OTR) oxytocin Gq chimera (mGoqi) complex -

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Basic information

Entry
Database: PDB / ID: 7qvm
TitleHuman Oxytocin receptor (OTR) oxytocin Gq chimera (mGoqi) complex
Components
  • (Guanine nucleotide-binding protein ...) x 3
  • Antibody fragment scFv16
  • Oxytocin
  • Oxytocin receptor
KeywordsSIGNALING PROTEIN / GPCR / OTR / G protein / OT / scFv16 / mGoqi / oxytocin / membrane protein
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 / sperm ejaculation / positive regulation of penile erection / positive regulation of uterine smooth muscle contraction ...oxytocin receptor activity / positive regulation of hindgut contraction / maternal aggressive behavior / response to anoxia / oxytocin receptor binding / neurohypophyseal hormone activity / V1A vasopressin receptor binding / sperm ejaculation / positive regulation of penile erection / positive regulation of uterine smooth muscle contraction / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / maternal process involved in parturition / positive regulation of norepinephrine secretion / negative regulation of urine volume / drinking behavior / telencephalon development / response to sucrose / grooming behavior / positive regulation of prostaglandin secretion / response to ether / mu-type opioid receptor binding / positive regulation of blood pressure / corticotropin-releasing hormone receptor 1 binding / neuropeptide hormone activity / maternal behavior / positive regulation of ossification / positive regulation of female receptivity / vesicle docking involved in exocytosis / positive regulation of synapse assembly / digestive tract development / response to food / G protein-coupled dopamine receptor signaling pathway / eating behavior / male mating behavior / regulation of heart contraction / parallel fiber to Purkinje cell synapse / suckling behavior / neuronal dense core vesicle / social behavior / microvillus / peptide hormone binding / positive regulation of synaptic transmission / postsynaptic modulation of chemical synaptic transmission / response to retinoic acid / negative regulation of insulin secretion / response to electrical stimulus / cellular response to hormone stimulus / response to glucocorticoid / estrous cycle / response to cAMP / ionotropic glutamate receptor binding / response to prostaglandin E / G protein-coupled serotonin receptor binding / adenylate cyclase regulator activity / adenylate cyclase-inhibiting serotonin receptor signaling pathway / negative regulation of blood pressure / muscle contraction / positive regulation of vasoconstriction / lactation / ERK1 and ERK2 cascade / response to amphetamine / response to cytokine / positive regulation of synaptic transmission, glutamatergic / regulation of heart rate / secretory granule / response to progesterone / response to activity / positive regulation of synaptic transmission, GABAergic / GABA-ergic synapse / female pregnancy / adherens junction / locomotory behavior / response to cocaine / terminal bouton / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / memory / response to peptide hormone / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / Activation of the phototransduction cascade / 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 / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through CDC42 / Glucagon signaling in metabolic regulation / 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
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 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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. / P-loop containing nucleotide triphosphate hydrolases / WD domain, G-beta repeat / 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
G protein subunit alpha o1 / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsWaltenspuhl, Y. / Ehrenmann, J. / Vacca, S. / Thom, C. / Medalia, O. / Pluckthun, A.
Funding support Switzerland, 1items
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, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 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
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
G: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
L: Oxytocin
R: Oxytocin receptor
S: Antibody fragment scFv16


Theoretical massNumber of molelcules
Total (without water)140,0636
Polymers140,0636
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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

#1: Protein 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


Mass: 25650.412 Da / Num. of mol.: 1
Mutation: E9D,R10K,L13V,A18M,I344L,A345Q,N346L,G350E,C351Y,G352N,Y354V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNAO1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: A0A1W2PS82, UniProt: B3KP89, UniProt: P09471
#2: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Transducin beta chain 1


Mass: 39086.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNB1 / 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 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P59768

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Protein/peptide / Protein / Antibody , 3 types, 3 molecules LRS

#4: Protein/peptide Oxytocin / Ocytocin


Mass: 1008.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01178
#5: Protein Oxytocin receptor / OT-R


Mass: 39777.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OXTR / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P30559
#6: Antibody Antibody fragment scFv16


Mass: 26679.721 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm)

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1OTR in complex with Oxytocin, heterotrimeric mini-Gq chimera (Goqi) and scFv16COMPLEXall0RECOMBINANT
2Heterotrimeric mini-Gq chimera (Goqi) and Oxytocin receptorCOMPLEX#1-#3, #51RECOMBINANT
3OxytocinCOMPLEX#41RECOMBINANT
4Antibody fragment scFv16COMPLEX#61RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Homo sapiens (human)9606
44Mus musculus (house mouse)10090
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Spodoptera frugiperda (fall armyworm)7108
33Synthetic construct (others)32630
44Spodoptera frugiperda (fall armyworm)7108
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 63.78 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: Gctf / Category: CTF correction
CTF correctionType: NONE
3D reconstructionResolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 392369 / Symmetry type: POINT

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