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- PDB-7otd: Oxytocin NMR solution structure -

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Basic information

Entry
Database: PDB / ID: 7otd
TitleOxytocin NMR solution structure
ComponentsUNK-TYR-ILE-GLN-ASN-CYS-PRO-LEU-GLY
KeywordsHORMONE / natural peptide / cyclic / disulfide bond / copper-binding
Function / homologyCOPPER (II) ION / AMINO GROUP
Function and homology information
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
DepositionJun 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UNK-TYR-ILE-GLN-ASN-CYS-PRO-LEU-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,0903
Polymers1,0101
Non-polymers802
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study, Amide proton signal was lost and paramagnetic relaxation enhancement was noted for the bound residues.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1280 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide UNK-TYR-ILE-GLN-ASN-CYS-PRO-LEU-GLY


Mass: 1010.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Oxytocin bound to copper II / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Details: Oxytocin bound to copper II / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-NH2 / AMINO GROUP


Mass: 16.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NH2 / Details: Oxytocin bound to copper II / Source: (synth.) Homo sapiens (human)

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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: 3.3 mM oxytocin, 5 mM ammonium acetate buffer, 10 % v/v [U-100% 2H] D2O, 90 % v/v H2O, 0.33 mM CuCl2, 90% H2O/10% D2O
Details: Copper chloride was added to obtain the copper II complex equilibrium. The solution was filtered before adding the peptide to reduce microbial growth.
Label: OT+Cu / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
3.3 mMoxytocinnatural abundance1
5 mMammonium acetate buffernatural abundance1
10 % v/vD2O[U-100% 2H]1
90 % v/vH2Onatural abundance1
0.33 mMCuCl2natural abundance1
Sample conditionsIonic strength: 14.9 mM / Label: ot-cu / pH: 6.7 pH* / Pressure: 1 atm / Temperature: 293.2 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 500 MHz

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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
TopSpinBruker Biospincollection
NMRFAM-SPARKY1.47Lee, W.; Tonelli, M.; Markley, J. L. NMRFAM-SPARKY: Enhanced Software for Biomolecular NMR Spectroscopy. Bioinformatics 2015, 31 (8), 1325-1327.peak picking
NMRFAM-SPARKY1.47Lee, W.; Tonelli, M.; Markley, J. L. NMRFAM-SPARKY: Enhanced Software for Biomolecular NMR Spectroscopy. Bioinformatics 2015, 31 (8), 1325-1327.chemical shift assignment
NMRFAM-SPARKY1.47Lee, W.; Tonelli, M.; Markley, J. L. NMRFAM-SPARKY: Enhanced Software for Biomolecular NMR Spectroscopy. Bioinformatics 2015, 31 (8), 1325-1327.chemical shift assignment
CNSSchwieters, C. D.; Kuszewski, J. J.; Tjandra, N.; Clore, G. M. The Xplor-NIH NMR Molecular Structure Determination Package. J. Magn. Reson. 2003, 160 (1), 65structure calculation
UCSF Chimera1.14Pettersen, E. F.; Goddard, T. D.; Huang, C. C.; Couch, G. S.; Greenblatt, D. M.; Meng, E. C.; Ferrin, T. E. UCSF Chimera - A Visualization System for Exploratory Research and Analysis. J. Comput. Chem. 2004, 25 (13), 1605-1612.data analysis
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 5 / Details: XPLOR-NIH
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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