BMRB Entry 18971

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR18971
MolProbity Validation Chart

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Title:
Structure and dynamics of a human Nedd4 WW domain-ENaC complex
Deposition date:
2013-01-23
Original release date:
2013-06-04
Authors:
Bobby, Romel; Medini, Karima; Neudecker, Philipp; Lee, Verne; MacDonald, Fiona; Brimble, Margaret; Lott, J. Shaun; Dingley, Andrew
Citation:

Citation: Bobby, Romel; Medini, Karima; Neudecker, Philipp; Lee, Tet Verne; Brimble, Margaret; McDonald, Fiona; Lott, J. Shaun; Dingley, Andrew. "Structure and dynamics of human Nedd4-1 WW3 in complex with the ENaC PY motif."  Biochim. Biophys. Acta 1834, 1632-1641 (2013).
PubMed: 23665454

Assembly members:

Assembly members:
Nedd4_WW3*_domain, polymer, 43 residues, 4971.661 Da.
alpha_ENaC_PY_peptide, polymer, 11 residues, 1058.196 Da.

Natural source:

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

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET42

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Nedd4_WW3*_domain: GSMEQGFLPKGWEVRHAPNG RPFFIDHNTKTTTWEDPRLK IPA
alpha_ENaC_PY_peptide: TAPPPAYATLG

Data typeCount
13C chemical shifts219
15N chemical shifts60
1H chemical shifts361
heteronuclear NOE values102
order parameters34
T1 relaxation values102
T2 relaxation values102

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1Nedd4_WW3*_domain1
2alpha_ENaC_PY_peptide2

Entities:

Entity 1, Nedd4_WW3*_domain 43 residues - 4971.661 Da.

Residues G416-E419 in NMR structure represent non-native residues from the expression vector

1   GLYSERMETGLUGLNGLYPHELEUPROLYS
2   GLYTRPGLUVALARGHISALAPROASNGLY
3   ARGPROPHEPHEILEASPHISASNTHRLYS
4   THRTHRTHRTRPGLUASPPROARGLEULYS
5   ILEPROALA

Entity 2, alpha_ENaC_PY_peptide 11 residues - 1058.196 Da.

1   THRALAPROPROPROALATYRALATHRLEU
2   GLY

Samples:

sample_1: Nedd4 WW3* domain, [U-99% 13C; U-99% 15N], 1.1 mM; alpha ENaC PY peptide 2.2 mM; sodium phosphate 20 mM; sodium azide 0.1%; TSP 1 mM; H2O 93%; D2O 7%

sample_2: Nedd4 WW3* domain 3.0 mM; alpha ENaC PY peptide, [U-99% 13C; U-99% 15N], 1.5 mM; sodium phosphate 20 mM; sodium azide 0.1%; TSP 1.0 mM; H2O 93%; D2O 7%

sample_3: Nedd4 WW3* domain, [U-99% 15N], 1.61 mM; alpha ENaC PY peptide 4.38 mM; sodium phosphate 20 mM; sodium azide 0.1%; TSP 1 mM; H2O 93%; D2O 7%

sample_conditions_1: ionic strength: 0.02 M; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
2D CBCA(CO)NHsample_2isotropicsample_conditions_1
2D C(CO)NHsample_2isotropicsample_conditions_1
2D HNCOsample_2isotropicsample_conditions_1
2D HNCACBsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D 1H-15N TOCSYsample_2isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
2D 1H-15N NOESYsample_2isotropicsample_conditions_1
2D 1H-13C NOESYsample_2isotropicsample_conditions_1
3D 15N/13C-EDITED NOESYsample_2isotropicsample_conditions_1
2D 13C-edited/filtered NOESYsample_2isotropicsample_conditions_1
2D long-range HNCOsample_1isotropicsample_conditions_1
2D 1H-15N R2 relaxationsample_3isotropicsample_conditions_1
2D 1H-15N R1 relaxationsample_3isotropicsample_conditions_1
2D 1H-15N heteronuclear NOEsample_3isotropicsample_conditions_1
2D 1H-15N R1rho relaxationsample_3isotropicsample_conditions_1
2D 1H-15N R1 relaxationsample_3isotropicsample_conditions_1
2D 1H-15N heteronuclear NOEsample_3isotropicsample_conditions_1
2D 1H-15N R1rho relaxationsample_3isotropicsample_conditions_1
2D 1H-15N R1 relaxationsample_3isotropicsample_conditions_1
2D 1H-15N heteronuclear NOEsample_3isotropicsample_conditions_1
3D HCANsample_1isotropicsample_conditions_1
2D HCANsample_2isotropicsample_conditions_1
2D HBCBCGCDHDsample_1isotropicsample_conditions_1
2D HBCBCGCDCEHEsample_1isotropicsample_conditions_1
2D HBCBCACONHANsample_2isotropicsample_conditions_1
2D HBCBCACONHACAsample_2isotropicsample_conditions_1
2D 15N CPMG dispersionsample_3isotropicsample_conditions_1
2D 15N CPMG dispersionsample_3isotropicsample_conditions_1

Software:

TOPSPIN v2.1pl3, Bruker Biospin - collection

CcpNMR v2.07, CCPN - chemical shift assignment, peak picking

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

Relax v2.0.0, d'Auvergne, E. J. and Gooley, P. R. - data analysis

NMR spectrometers:

  • Bruker Avance 600 MHz
  • Varian Direct Drive 800 MHz
  • Varian Direct Drive 900 MHz
  • Varian Unity-INOVA 600 MHz

Related Database Links:

NCBI 4734
BMRB 16574 16575
PDB
REF XP_010008470 XP_011758823 XP_012325247
UNP P37088
AlphaFold Q9UM64

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