[English] 日本語
Yorodumi
- EMDB-14180: Human Oxytocin receptor (OTR) oxytocin Gq chimera (mGoqi) complex -

+
Open data


ID or keywords:

Loading...

-
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
Function / homology
Function and homology information


oxytocin receptor activity / positive regulation of hindgut contraction / response to anoxia / maternal aggressive behavior / oxytocin receptor binding / neurohypophyseal hormone activity / V1A vasopressin receptor binding / guanyl nucleotide binding / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin ...oxytocin receptor activity / positive regulation of hindgut contraction / response to anoxia / maternal aggressive behavior / oxytocin receptor binding / neurohypophyseal hormone activity / V1A vasopressin receptor binding / guanyl nucleotide binding / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / maternal process involved in parturition / response to prostaglandin E / positive regulation of penile erection / positive regulation of uterine smooth muscle contraction / positive regulation of norepinephrine secretion / negative regulation of urine volume / sperm ejaculation / telencephalon development / response to sucrose / drinking behavior / positive regulation of prostaglandin secretion / grooming behavior / response to ether / positive regulation of blood pressure / maternal behavior / neuropeptide hormone activity / positive regulation of ossification / digestive tract development / 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 / regulation of heart contraction / eating behavior / male mating behavior / suckling behavior / peptide hormone binding / microvillus / social behavior / mu-type opioid receptor binding / estrous cycle / corticotropin-releasing hormone receptor 1 binding / negative regulation of insulin secretion / positive regulation of synaptic transmission / G protein-coupled serotonin receptor binding / response to electrical stimulus / response to retinoic acid / response to glucocorticoid / positive regulation of vasoconstriction / cellular response to hormone stimulus / response to cAMP / response to amphetamine / ERK1 and ERK2 cascade / negative regulation of blood pressure / lactation / regulation of heart rate / positive regulation of synaptic transmission, glutamatergic / response to cocaine / secretory granule / response to activity / response to cytokine / locomotory behavior / muscle contraction / response to progesterone / positive regulation of synaptic transmission, GABAergic / female pregnancy / adherens junction / peptide binding / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / Activation of the phototransduction cascade / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G-protein activation / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / terminal bouton / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / memory / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Sensory perception of sweet, bitter, and umami (glutamate) taste / response to peptide hormone / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / 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 / 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. / 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 / cDNA FLJ31446 fis, clone NT2NE2000909, highly similar to Guanine nucleotide-binding protein G(o) subunit alpha 1 / 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 / Vacca S / Thom C / Medalia O / Pluckthun A
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-
UpdateAug 10, 2022-
Current statusAug 10, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_14180.png

Downloads & links

-
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
Others
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.)-2.4180672e-05 (±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 °

-
Supplemental data

-
Additional map: raw map

Fileemd_14180_additional_1.map
Annotationraw map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
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

+
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 / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all

+
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)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

+
Supramolecule #3: Oxytocin

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

+
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)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

+
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

+
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

+
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

+
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)

+
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

+
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
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

-
Image processing

CTF correctionSoftware - Name: Gctf
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more