BMRB Entry 25000

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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/BMR25000
MolProbity Validation Chart

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Title:
WW3 domain of Nedd4L in complex with its HECT domain PY motif
Deposition date:
2014-06-02
Original release date:
2014-10-20
Authors:
Escobedo, Albert; Macias, Maria; Gomes, Tiago; Aragon, Eric; Martin-Malpartida, Pau; Ruiz, Lidia
Citation:

Citation: Escobedo, Albert; Gomes, Tiago; Aragon, Eric; Martin-Malpartida, Pau; Ruiz, Lidia; Macias, Maria. "Structural Basis of the Activation and Degradation Mechanisms of the E3 Ubiquitin Ligase Nedd4L"  Structure 22, 1446-1457 (2014).
PubMed: 25295397

Assembly members:

Assembly members:
WW3, polymer, 48 residues, 3833.352 Da.
HECT_PY, polymer, 16 residues, 1608.784 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: recombinant technology   Host organism: Escherichia coli   Vector: pETM11

Entity Sequences (FASTA):

Entity Sequences (FASTA):
WW3: GAMEQSFLPPGWEMRIAPNG RPFFIDHNTKTTTWEDPRLK FPVHMRSK
HECT_PY: RLDLPPYETFEDLREK

Data typeCount
1H chemical shifts280
13C chemical shifts59
15N chemical shifts27

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1WW31
2HECT_PY2

Entities:

Entity 1, WW3 48 residues - 3833.352 Da.

Sequence numbering as in isoform 5

1   GLYALAMETGLUGLNSERPHELEUPROPRO
2   GLYTRPGLUMETARGILEALAPROASNGLY
3   ARGPROPHEPHEILEASPHISASNTHRLYS
4   THRTHRTHRTRPGLUASPPROARGLEULYS
5   PHEPROVALHISMETARGSERLYS

Entity 2, HECT_PY 16 residues - 1608.784 Da.

Sequence numbering as in isoform 5

1   ARGLEUASPLEUPROPROTYRGLUTHRPHE
2   GLUASPLEUARGGLULYS

Samples:

sample_1: WW3 0.7 mM; HECT_PY 1.4 mM; sodium chloride 150 mM; sodium phosphate 20 mM; H2O 90%; D2O 10%

sample_2: WW3, [U-100% 15N], 1 mM; HECT_PY 2 mM; sodium chloride 150 mM; sodium phosphate 20 mM; H2O 90%; D2O 10%

sample_3: WW3, [U-100% 13C; U-100% 15N], 0.8 mM; HECT_PY 1.6 mM; sodium chloride 150 mM; sodium phosphate 20 mM; H2O 90%; D2O 10%

sample_conditions_1: temperature: 298 K; pH: 7; pressure: 1 atm

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D 1H-15N TOCSYsample_2isotropicsample_conditions_1
3D HNCACBsample_3isotropicsample_conditions_1
3D CBCA(CO)NHsample_3isotropicsample_conditions_1

Software:

CNSSOLVE, Brunger, Adams, Clore, Gros, Nilges and Read - refinement, structure solution

CARA, Keller and Wuthrich - chemical shift assignment, peak picking

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

TOPSPIN, Bruker Biospin - collection

TALOS, Cornilescu, Delaglio and Bax - geometry optimization

NMR spectrometers:

  • Bruker Avance 600 MHz

Related Database Links:

UNP Q96PU5 Q96PU5
BMRB 17529
PDB
DBJ BAA23711 BAB69424 BAC31307 BAE37373 BAG11191
EMBL CAB70754 CAH90908
GB AAG43524 AAH00621 AAH19345 AAH32597 AAH39746
REF NP_001008301 NP_001107858 NP_001125518 NP_001138436 NP_001138437
SP Q5RBF2 Q8CFI0 Q96PU5
TPG DAA15876
AlphaFold Q9NT88 Q9NT88 Q5RBF2 Q8CFI0 Q96PU5