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Biological Magnetic Resonance Data Bank


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BMRB Entry 11578

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR11578
MolProbity Validation Chart

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Title: Solution structure of the complex between p53 transactivation domain 2 and TFIIH p62 PH domain   PubMed: 25216154

Deposition date: 2014-09-24 Original release date: 2017-08-11

Authors: Okuda, Masahiko; Nishimura, Yoshifumi

Citation: Okuda, Masahiko; Nishimura, Yoshifumi. "Extended String Binding Mode of the Phosphorylated Transactivation Domain of Tumor Suppressor p53"  J. Am. Chem. Soc. ., 14143-14152 (2014).

Assembly members:
p53_TAD2, polymer, 22 residues, 2724.623 Da.
TFIIH_p62_PH_domain, polymer, 110 residues, 12306.429 Da.

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

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
p53_TAD2: DDLMLXPDDIEQWFXEDPGP DE
TFIIH_p62_PH_domain: GSMATSSEEVLLIVKKVRQK KQDGALYLMAERIAWAPEGK DRFTISHMYADIKCQKISPE GKAKIQLQLVLHAGDTTNFH FSNESTAVKERDAVKDLLQQ LLPKFKRKAN

Data sets:
Data typeCount
13C chemical shifts497
15N chemical shifts116
1H chemical shifts911

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22

Entities:

Entity 1, entity_1 22 residues - 2724.623 Da.

1   ASPASPLEUMETLEUSEPPROASPASPILE
2   GLUGLNTRPPHETPOGLUASPPROGLYPRO
3   ASPGLU

Entity 2, entity_2 110 residues - 12306.429 Da.

Residues 1,2 represent a non-native remainder of an affinity tag

1   GLYSERMETALATHRSERSERGLUGLUVAL
2   LEULEUILEVALLYSLYSVALARGGLNLYS
3   LYSGLNASPGLYALALEUTYRLEUMETALA
4   GLUARGILEALATRPALAPROGLUGLYLYS
5   ASPARGPHETHRILESERHISMETTYRALA
6   ASPILELYSCYSGLNLYSILESERPROGLU
7   GLYLYSALALYSILEGLNLEUGLNLEUVAL
8   LEUHISALAGLYASPTHRTHRASNPHEHIS
9   PHESERASNGLUSERTHRALAVALLYSGLU
10   ARGASPALAVALLYSASPLEULEUGLNGLN
11   LEULEUPROLYSPHELYSARGLYSALAASN

Samples:

sample_1: TFIIH p62 PH domain, [U-99% 13C; U-99% 15N], 0.4 mM; p53 TAD2 0.48 mM; potassium phosphate 20 mM; DTT, [U-2H], 5 mM; H2O 90%; D2O, [U-2H], 10%

sample_2: TFIIH p62 PH domain, [U-99% 13C; U-99% 15N], 0.4 mM; p53 TAD2 0.48 mM; potassium phosphate 20 mM; DTT, [U-2H], 5 mM; D2O, [U-2H], 100%

sample_conditions_1: ionic strength: 20 mM; pH: 6.8; pressure: 1 atm; temperature: 305 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_2isotropicsample_conditions_1
3D HNHBsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1

Software:

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

NMRView, Johnson, One Moon Scientific - chemical shift assignment

X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

Molmol, Koradi, Billeter and Wuthrich - data analysis

ProcheckNMR, Laskowski and MacArthur - data analysis

NMR spectrometers:

  • Bruker Avance 800 MHz
  • Bruker Avance 600 MHz