BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 18842

Title: NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and Rad4   PubMed: 23295669

Authors: Lafrance-Vanasse, Julien; Arseneault, Genevieve; Cappadocia, Laurent; Legault, Pascale; Omichinski, James

Citation: Lafrance-Vanasse, Julien; Arseneault, Genevieve; Cappadocia, Laurent; Legault, Pascale; Omichinski, James. "Structural and functional evidence that Rad4 competes with Rad2 for binding to the Tfb1 subunit of TFIIH in NER."  Nucleic Acids Res. 41, 2736-2745 (2013).

Assembly members:
Tfb1, polymer, 119 residues, 12903.807 Da.
Rad4, polymer, 42 residues, 1747.696 Da.

Natural source:   Common Name: baker   Taxonomy ID: 4932   Superkingdom: not available   Kingdom: not available   Genus/species: Eukaryota Fungi

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

Entity Sequences (FASTA):
Tfb1: PSHSGAAIFEKVSGIIAINE DVSPAELTWRSTDGDKVHTV VLSTIDKLQATPASSEKMML RLIGKVDESKKRKDNEGNEV VPKPQRHMFSFNNRTVMDNI KMTLQQIISRYKDADGNSS
Rad4: GSTDDSVEEIQSSEEDYDSE EFEDVTDGNEVAGVEDISVE IK

Data sets:
Data typeCount
13C chemical shifts552
15N chemical shifts144
1H chemical shifts862

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Tfb11
2Rad42

Entities:

Entity 1, Tfb1 119 residues - 12903.807 Da.

1   PROSERHISSERGLYALAALAILEPHEGLU
2   LYSVALSERGLYILEILEALAILEASNGLU
3   ASPVALSERPROALAGLULEUTHRTRPARG
4   SERTHRASPGLYASPLYSVALHISTHRVAL
5   VALLEUSERTHRILEASPLYSLEUGLNALA
6   THRPROALASERSERGLULYSMETMETLEU
7   ARGLEUILEGLYLYSVALASPGLUSERLYS
8   LYSARGLYSASPASNGLUGLYASNGLUVAL
9   VALPROLYSPROGLNARGHISMETPHESER
10   PHEASNASNARGTHRVALMETASPASNILE
11   LYSMETTHRLEUGLNGLNILEILESERARG
12   TYRLYSASPALAASPGLYASNSERSER

Entity 2, Rad4 42 residues - 1747.696 Da.

1   GLYSERTHRASPASPSERVALGLUGLUILE
2   GLNSERSERGLUGLUASPTYRASPSERGLU
3   GLUPHEGLUASPVALTHRASPGLYASNGLU
4   VALALAGLYVALGLUASPILESERVALGLU
5   ILELYS

Samples:

sample_1: Tfb1, [U-100% 13C; U-100% 15N], 1 mM; Rad4 1.25 mM; sodium phosphate 20 mM; EDTA 1 mM; DTT 1 mM

sample_2: Tfb1, [U-100% 13C; U-100% 15N], 1 mM; Rad4 1.25 mM; sodium phosphate 20 mM; EDTA 1 mM; DTT 1 mM

sample_3: Tfb1, [U-100% 15N], 1 mM; Rad4 1.25 mM; sodium phosphate 20 mM; EDTA 1 mM; DTT 1 mM

sample_4: Tfb1 1.25 mM; Rad4, [U-100% 13C; U-100% 15N], 1 mM; sodium phosphate 20 mM; EDTA 1 mM; DTT 1 mM

sample_5: Tfb1 1.25 mM; Rad4, [U-100% 13C; U-100% 15N], 1 mM; sodium phosphate 20 mM; EDTA 1 mM; DTT 1 mM

sample_6: Tfb1 1.25 mM; Rad4, [U-100% 15N], 1 mM; sodium phosphate 20 mM; EDTA 1 mM; DTT 1 mM

sample_conditions_1: ionic strength: 20 mM; pH: 6.5; pressure: 1 atm; temperature: 300 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_3isotropicsample_conditions_1
2D 1H-15N HSQCsample_6isotropicsample_conditions_1
2D 1H-13C HSQCsample_5isotropicsample_conditions_1
3D CBCA(CO)NHsample_4isotropicsample_conditions_1
3D HNCOsample_4isotropicsample_conditions_1
3D HNCACBsample_4isotropicsample_conditions_1
3D H(CCO)NHsample_4isotropicsample_conditions_1
3D HCCH-COSYsample_5isotropicsample_conditions_1
3D 1H-15N NOESYsample_6isotropicsample_conditions_1
3D 1H-13C NOESYsample_5isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D HCCH-COSYsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_3isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1

Software:

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

VNMR, Varian - collection

VNMRJ, Varian - collection

NMRView, Johnson, One Moon Scientific - data analysis

TALOS, Cornilescu, Delaglio and Bax - data analysis

NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis

CcpNMR_2.1, CCPN - chemical shift assignment, data analysis, peak picking

NMR spectrometers:

  • Varian INOVA 500 MHz
  • Varian INOVA 600 MHz
  • Varian INOVA 800 MHz

Related Database Links:

BMRB 18229 19791 25540
PDB
DBJ GAA22531
EMBL CAY78811
GB AAA35143 AAB64747 AAU09707 AHY75284 AJP38011 AAA34944 AAA34945 AAB64689 AHY75718 EDN63138
REF NP_010597 NP_011089
SP P32776 P14736
TPG DAA12150 DAA07824