BMRB Entry 25597

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25597
MolProbity Validation Chart

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Title:
Solution NMR structure of Dynorphin 1-13 bound to Kappa Opioid Receptor
Deposition date:
2015-05-06
Original release date:
2015-09-10
Authors:
O'Connor, Casey; White, Kate; Doncescu, Nathalie; Didenko, Tatiana; Roth, Bryan; Czaplicki, Georges; Stevens, Raymond; Wuthrich, Kurt; Milon, Alain
Citation:

Citation: O'Connor, Casey; White, Kate; Doncescu, Nathalie; Didenko, Tatiana; Roth, Bryan; Czaplicki, Georges; Stevens, Raymond; Wuthrich, Kurt; Milon, Alain. "NMR structure and dynamics of the agonist dynorphin peptide bound to the human kappa opioid receptor"  Proc. Natl. Acad. Sci. U.S.A. 112, 11852-11857 (2015).
PubMed: 26372966

Assembly members:

Assembly members:
Dynorphin_1-13, polymer, 13 residues, 1609.012 Da.

Natural source:

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Dynorphin_1-13: YGGFLRRIRPKLK

Data sets:
Data typeCount
13C chemical shifts18
15N chemical shifts18
1H chemical shifts125

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1entity1

Entities:

Entity 1, entity 13 residues - 1609.012 Da.

1   TYRGLYGLYPHELEUARGARGILEARGPRO
2   LYSLEULYS

Samples:

sample_1: Dynorphin 1-13, [U-15N-GFLI], 1 mM; potassium chloride 150 mM; MES, [U-2H], 40 mM; DSS 100 uM; KOR 10 uM; DDM 8 mM; CHS 1.6 mM; H2O 90%; D2O 10%

sample_2: Dynorphin 1-13, [U-15N-GFLIR; U-13C-R], 1 mM; potassium chloride 150 mM; MES, [U-2H], 40 mM; DSS 100 uM; KOR 10 uM; DDM 8 mM; CHS 1.6 mM; H2O 90%; D2O 10%

sample_conditions_1: pH: 6.1; pressure: 1 atm; temperature: 280 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
2D HNCACBsample_2isotropicsample_conditions_1
15N T1 T2 hetNOEsample_1isotropicsample_conditions_1
15N T2sample_2isotropicsample_conditions_1

Software:

TOPSPIN v3.2, Bruker Biospin - chemical shift assignment, peak picking, processing

AMBER v14, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - geometry optimization, structure solution

NMR spectrometers:

  • Bruker Avance III 800 MHz
  • Bruker Avance 800 MHz
  • Bruker Avance III 700 MHz
  • Bruker Avance III 600 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks