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- PDB-6tpk: Crystal structure of the human oxytocin receptor -

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Basic information

Entry
Database: PDB / ID: 6tpk
TitleCrystal structure of the human oxytocin receptor
ComponentsOxytocin receptor
KeywordsHORMONE RECEPTOR / Eukaryotic / Protein
Function / homology
Function and homology information


oxytocin receptor activity / response to anoxia / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / maternal process involved in parturition / positive regulation of penile erection / positive regulation of uterine smooth muscle contraction / positive regulation of norepinephrine secretion / sperm ejaculation ...oxytocin receptor activity / response to anoxia / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / maternal process involved in parturition / positive regulation of penile erection / positive regulation of uterine smooth muscle contraction / positive regulation of norepinephrine secretion / sperm ejaculation / telencephalon development / positive regulation of blood pressure / maternal behavior / digestive tract development / positive regulation of synapse assembly / eating behavior / suckling behavior / peptide hormone binding / microvillus / social behavior / estrous cycle / positive regulation of vasoconstriction / cellular response to hormone stimulus / response to amphetamine / ERK1 and ERK2 cascade / lactation / positive regulation of synaptic transmission, glutamatergic / response to cocaine / response to cytokine / muscle contraction / response to progesterone / positive regulation of synaptic transmission, GABAergic / female pregnancy / adherens junction / peptide binding / memory / response to peptide hormone / response to estradiol / positive regulation of cold-induced thermogenesis / heart development / positive regulation of cytosolic calcium ion concentration / G alpha (q) signalling events / cell surface receptor signaling pathway / response to xenobiotic stimulus / G protein-coupled receptor signaling pathway / apical plasma membrane / plasma membrane
Similarity search - Function
Oxytocin receptor / Vasopressin receptor / 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)
Similarity search - Domain/homology
CHOLESTEROL / Chem-NU2 / DI(HYDROXYETHYL)ETHER / Oxytocin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsWaltenspuehl, Y. / Schoeppe, J. / Ehrenmann, J. / Kummer, L. / Plueckthun, A.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_153143 Switzerland
Swiss National Science Foundation31003A_182334 Switzerland
CitationJournal: Sci Adv / Year: 2020
Title: Crystal structure of the human oxytocin receptor.
Authors: Waltenspuhl, Y. / Schoppe, J. / Ehrenmann, J. / Kummer, L. / Pluckthun, A.
History
DepositionDec 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Sep 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oxytocin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1504
Polymers56,1631
Non-polymers9873
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint7 kcal/mol
Surface area22990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.987, 78.858, 283.486
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Oxytocin receptor / OT-R


Mass: 56162.547 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
#2: Chemical ChemComp-NU2 / (3~{R},6~{R})-6-[(2~{S})-butan-2-yl]-3-(2,3-dihydro-1~{H}-inden-2-yl)-1-[(1~{R})-1-(2-methyl-1,3-oxazol-4-yl)-2-morpholin-4-yl-2-oxidanylidene-ethyl]piperazine-2,5-dione


Mass: 494.583 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H34N4O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: antagonist*YM
#3: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.13 Å3/Da / Density % sol: 70.19 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase / Details: ADA, PEG400, NaH2PO4, TCEP

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Data collection

DiffractionMean temperature: 104.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 17, 2019
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→47.59 Å / Num. obs: 14739 / % possible obs: 99.9 % / Redundancy: 32.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.489 / Net I/σ(I): 7.5 / Num. measured all: 472505 / Scaling rejects: 91
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
3.2-3.4232.95.3598606326160.5781.199.7
9.05-47.5930.40.105221757300.99824.899.4

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: protein

Resolution: 3.2→29.843 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.22
RfactorNum. reflection% reflection
Rfree0.2655 632 4.33 %
Rwork0.2518 --
obs0.2523 14602 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 236.69 Å2 / Biso mean: 100.8851 Å2 / Biso min: 45.72 Å2
Refinement stepCycle: final / Resolution: 3.2→29.843 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3647 0 71 0 3718
Biso mean--113.37 --
Num. residues----461
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.2002-3.4470.38791100.356276399
3.447-3.79320.33961320.30352705100
3.7932-4.34070.25461370.24572774100
4.3407-5.46330.21691340.22052805100
5.4633-29.840.25061190.23332923100
Refinement TLS params.Method: refined / Origin x: 4.3397 Å / Origin y: -4.7867 Å / Origin z: 95.9716 Å
111213212223313233
T0.8463 Å2-0.0644 Å2-0.1016 Å2-0.7631 Å2-0.0439 Å2--0.6253 Å2
L1.4834 °2-0.4247 °2-1.7558 °2-1.3284 °21.1086 °2--4.2439 °2
S0.1516 Å °-0.4108 Å °0.1207 Å °0.5507 Å °-0.1271 Å °-0.2768 Å °-0.2222 Å °-0.1177 Å °0.0003 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA35 - 1196
2X-RAY DIFFRACTION1allA1501 - 1701

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