BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 11594

Title: Solution structure of the complex between XPC acidic domain and TFIIH p62 PH domain   PubMed: 26278177

Deposition date: 2015-07-01 Original release date: 2016-02-15

Authors: Okuda, Masahiko; Nishimura, Yoshifumi

Citation: Okuda, Masahiko; Kinoshita, Minoru; Kakumu, Erina; Sugasawa, Kaoru; Nishimura, Yoshifumi. "Structural Insight into the Mechanism of TFIIH Recognition by the Acidic String of the Nucleotide Excision Repair Factor XPC"  Structure 23, 1827-1837 (2015).

Assembly members:
XPC_acidic_domain, polymer, 52 residues, 5511.741 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: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
XPC_acidic_domain: GSHMAHHLKRGATMNEDSNE EEEESENDWEEVEELSEPVL GDVRESTAFSRS
TFIIH_p62_PH_domain: GSMATSSEEVLLIVKKVRQK KQDGALYLMAERIAWAPEGK DRFTISHMYADIKCQKISPE GKAKIQLQLVLHAGDTTNFH FSNESTAVKERDAVKDLLQQ LLPKFKRKAN

Data sets:
Data typeCount
13C chemical shifts680
15N chemical shifts165
1H chemical shifts1036

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1XPC acidic domain1
2TFIIH p62 PH domain2

Entities:

Entity 1, XPC acidic domain 52 residues - 5511.741 Da.

1   GLYSERHISMETALAHISHISLEULYSARG
2   GLYALATHRMETASNGLUASPSERASNGLU
3   GLUGLUGLUGLUSERGLUASNASPTRPGLU
4   GLUVALGLUGLULEUSERGLUPROVALLEU
5   GLYASPVALARGGLUSERTHRALAPHESER
6   ARGSER

Entity 2, TFIIH p62 PH domain 110 residues - 12306.429 Da.

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

sample_2: XPC acidic domain, [U-99% 13C; U-99% 15N], 0.4 mM; TFIIH p62 PH domain 0.48 mM; potassium phosphate 20 mM; DTT, [U-2H], 5 mM; D2O, [U-2H], 10%

sample_3: TFIIH p62 PH domain, [U-99% 13C; U-99% 15N], 0.4 mM; XPC acidic domain 0.48 mM; potassium phosphate 20 mM; DTT, [U-2H], 5 mM; H2O 90%; D2O, [U-2H], 10%

sample_4: TFIIH p62 PH domain, [U-99% 13C; U-99% 15N], 0.4 mM; XPC acidic domain 0.48 mM; potassium phosphate 20 mM; DTT, [U-2H], 5 mM; D2O, [U-2H], 10%

sample_conditions_1: ionic strength: 0.02 M; 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
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_3isotropicsample_conditions_1
2D 1H-13C HSQCsample_4isotropicsample_conditions_1
3D CBCA(CO)NHsample_3isotropicsample_conditions_1
3D HNCOsample_3isotropicsample_conditions_1
3D HBHA(CO)NHsample_3isotropicsample_conditions_1
3D HCCH-TOCSYsample_4isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_4isotropicsample_conditions_1
3D HNHBsample_3isotropicsample_conditions_1
3D 1H-15N NOESYsample_3isotropicsample_conditions_1
3D 1H-13C NOESYsample_4isotropicsample_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 700 MHz
  • Bruker Avance 600 MHz

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts