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- PDB-7ofg: Oxytocin NMR solution structure -

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Basic information

Entry
Database: PDB / ID: 7ofg
TitleOxytocin NMR solution structure
ComponentsOxytocin
KeywordsHORMONE / natural peptide / cyclic / disulfide bond
Function / homology
Function and homology information


positive regulation of hindgut contraction / maternal aggressive behavior / oxytocin receptor binding / neurohypophyseal hormone activity / V1A vasopressin receptor binding / Vasopressin-like receptors / response to prostaglandin E / positive regulation of uterine smooth muscle contraction / positive regulation of penile erection / positive regulation of norepinephrine secretion ...positive regulation of hindgut contraction / maternal aggressive behavior / oxytocin receptor binding / neurohypophyseal hormone activity / V1A vasopressin receptor binding / Vasopressin-like receptors / response to prostaglandin E / positive regulation of uterine smooth muscle contraction / positive regulation of penile erection / positive regulation of norepinephrine secretion / negative regulation of urine volume / sperm ejaculation / 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 / positive regulation of synapse assembly / positive regulation of female receptivity / response to food / eating behavior / male mating behavior / social behavior / positive regulation of synaptic transmission / response to retinoic acid / response to electrical stimulus / response to glucocorticoid / response to cAMP / negative regulation of blood pressure / response to amphetamine / regulation of heart rate / secretory granule / response to activity / response to progesterone / female pregnancy / response to cocaine / terminal bouton / 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 / signal transduction / extracellular space / extracellular region
Similarity search - Function
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
Similarity search - Domain/homology
Oxytocin-neurophysin 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsShalev, D.E. / Alshanski, I. / Yitzchaik, S. / Hurevich, M.
Funding support Israel, 1items
OrganizationGrant numberCountry
European Union (EU)664786 Israel
CitationJournal: J.Biol.Inorg.Chem. / Year: 2021
Title: Determining the structure and binding mechanism of oxytocin-Cu 2+ complex using paramagnetic relaxation enhancement NMR analysis.
Authors: Alshanski, I. / Shalev, D.E. / Yitzchaik, S. / Hurevich, M.
History
DepositionMay 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oxytocin


Theoretical massNumber of molelcules
Total (without water)1,0081
Polymers1,0081
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)14 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Oxytocin / Ocytocin


Mass: 1008.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Amidated C-terminus, Cys-Cys disulfide bond. / Source: (synth.) Homo sapiens (human) / References: UniProt: P01178
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H COSY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-1H ROESY

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Sample preparation

DetailsType: solution
Contents: 5 mM ammonium acetate, 3.3 mM Oxytocin, 90% H2O/10% D2O
Details: 3.3 mM oxytocin in 5 mM fresh ammonium acetate buffer, pH 6.7, in TDW, filtered at 2 micron with 10% deuterium oxide.
Label: OT/AA / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
5 mMammonium acetatenatural abundance1
3.3 mMOxytocinnatural abundance1
Sample conditionsDetails: Ammonium acetate buffer was used since it does not complex copper, however the buffer suffered from rapid bacterial growth within a couple of days and we had to prepare fresh samples for each experiment.
Ionic strength: 0.00665 M / Label: OT/AA / pH: 6.7 Not defined / PH err: 0.1 / Pressure: 1 atm / Temperature: 297.3 K / Temperature err: 0.1

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NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 500 MHz / Details: XYZ-gradients

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Processing

SoftwareName: UCSF ChimeraX / Version: 1.1/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: Windows / Type: package
NMR software
NameVersionDeveloperClassification
TopSpin3.6.2Bruker Biospincollection
NMRFAM-SPARKY1.47Lee, W.; Tonelli, M.; Markley, J. L.chemical shift assignment
CNS3.2Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
UCSF Chimera1.14Pettersen, E. F.; Goddard, T. D.; Huang, C. C.; Couch, G. S.; Greenblatt, D. M.; Meng, E. C.; Ferrin, T. E.data analysis
NMRFAM-SPARKY1.47Lee, W.; Tonelli, M.; Markley, J. L.peak picking
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 2 / Details: Based on 59 ROE restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 14

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