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- PDB-2n2f: Solution NMR structure of Dynorphin 1-13 bound to Kappa Opioid Re... -

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Basic information

Entry
Database: PDB / ID: 2n2f
TitleSolution NMR structure of Dynorphin 1-13 bound to Kappa Opioid Receptor
ComponentsDynorphin A(1-13)
KeywordsHORMONE RECEPTOR / GPCR
Function / homology
Function and homology information


opioid receptor binding / opioid peptide activity / Opioid Signalling / sensory perception / neuronal dense core vesicle / neuropeptide signaling pathway / axon terminus / hippocampal mossy fiber to CA3 synapse / Peptide ligand-binding receptors / G-protein activation ...opioid receptor binding / opioid peptide activity / Opioid Signalling / sensory perception / neuronal dense core vesicle / neuropeptide signaling pathway / axon terminus / hippocampal mossy fiber to CA3 synapse / Peptide ligand-binding receptors / G-protein activation / G alpha (i) signalling events / chemical synaptic transmission / neuronal cell body / dendrite / extracellular region / plasma membrane
Similarity search - Function
Proenkephalin B / Opioid neuropeptide precursor / Vertebrate endogenous opioids neuropeptide / Endogenous opioids neuropeptides precursors signature.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailsfewest violations, model2
AuthorsO'Connor, C. / White, K. / Doncescu, N. / Didenko, T. / Roth, B.L. / Czaplicki, G. / Stevens, R.C. / Wuthrich, K. / Milon, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: NMR structure and dynamics of the agonist dynorphin peptide bound to the human kappa opioid receptor.
Authors: O'Connor, C. / White, K.L. / Doncescu, N. / Didenko, T. / Roth, B.L. / Czaplicki, G. / Stevens, R.C. / Wuthrich, K. / Milon, A.
History
DepositionMay 6, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dynorphin A(1-13)


Theoretical massNumber of molelcules
Total (without water)1,6091
Polymers1,6091
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 1000structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Dynorphin A(1-13) / Proenkephalin-B / Beta-neoendorphin-dynorphin / Preprodynorphin


Mass: 1608.995 Da / Num. of mol.: 1 / Fragment: residues 207-219 / Source method: obtained synthetically
Details: SYNTHESIS OF THE PEPTIDE WAS PERFORMED BY A SOLID PHASE METHOD USING FMOC CHEMISTRY.
Source: (synth.) Homo sapiens (human) / References: UniProt: P01213

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1312D 1H-15N HSQC
1422D 1H-13C HSQC
1522D HN(CA)CB
16115N T1 T2 hetNOE
17215N T2

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-15N-GFLI] Dynorphin 1, 150 mM potassium chloride, 40 mM [U-2H] MES, 100 uM DSS, 10 uM KOR, 8 mM DDM, 1.6 mM CHS, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-15N-GFLIR; U-13C-R] Dynorphin 1, 150 mM potassium chloride, 40 mM [U-2H] MES, 100 uM DSS, 10 uM KOR, 8 mM DDM, 1.6 mM CHS, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMDynorphin 1-13-1[U-15N-GFLI]1
150 mMpotassium chloride-21
40 mMMES-3[U-2H]1
100 uMDSS-41
10 uMKOR-51
8 mMDDM-61
1.6 mMCHS-71
1 mMDynorphin 1-13-8[U-15N-GFLIR; U-13C-R]2
150 mMpotassium chloride-92
40 mMMES-10[U-2H]2
100 uMDSS-112
10 uMKOR-122
8 mMDDM-132
1.6 mMCHS-142
Sample conditionspH: 6.1 / Pressure: ambient / Temperature: 280 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker Avance IIIBrukerAVANCE III8001
Bruker AvanceBrukerAVANCE8002
Bruker Avance IIIBrukerAVANCE III7003
Bruker Avance IIIBrukerAVANCE III6004

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospinprocessing
TopSpin3.2Bruker Biospinpeak picking
TopSpin3.2Bruker Biospinchemical shift assignment
Amber14Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmangeometry optimization
Amber14Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanstructure solution
Amber14Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 56 / NOE medium range total count: 14 / NOE sequential total count: 42 / Protein phi angle constraints total count: 2 / Protein psi angle constraints total count: 2
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 1000 / Conformers submitted total number: 10
NMR ensemble rmsDistance rms dev: 0.2 Å

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