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 30243

Title: NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and the transactivation domain 1 of p65   PubMed: 28334776

Deposition date: 2017-02-11 Original release date: 2017-03-01

Authors: Lecoq, L.; Omichinski, J.; Raiola, L.; Cyr, N.; Chabot, P.; Arseneault, G.; Legault, P.

Citation: Lecoq, L.; Raiola, L.; Chabot, P.; Cyr, N.; Arseneault, G.; Legault, P.; Omichinski, J.. "Structural characterization of interactions between transactivation domain 1 of the p65 subunit of NF-kB and transcription regulatory factors"  Nucleic Acids Res. 45, 5564-5576 (2017).

Assembly members:
entity_1, polymer, 115 residues, 12903.701 Da.
entity_2, polymer, 33 residues, 3378.591 Da.

Natural source:   Common Name: baker's yeast   Taxonomy ID: 4932   Superkingdom: Eukaryota   Kingdom: Fungi   Genus/species: Saccharomyces cerevisiae

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

Entity Sequences (FASTA):
entity_1: PSHSGAAIFEKVSGIIAINE DVSPAELTWRSTDGDKVHTV VLSTIDKLQATPASSEKMML RLIGKVDESKKRKDNEGNEV VPKPQRHMFSFNNRTVMDNI KMTLQQIISRYKDAD
entity_2: GSPGYPNGLLSGDEDFSSIA DMDFSALLSQISS

Data sets:
Data typeCount
13C chemical shifts641
15N chemical shifts152
1H chemical shifts1019

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22

Entities:

Entity 1, entity_1 115 residues - 12903.701 Da.

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

Entity 2, entity_2 33 residues - 3378.591 Da.

1   GLYSERPROGLYTYRPROASNGLYLEULEU
2   SERGLYASPGLUASPPHESERSERILEALA
3   ASPMETASPPHESERALALEULEUSERGLN
4   ILESERSER

Samples:

sample_3: RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 1, [U-99% 13C; U-99% 15N], 0.8 mM; TRANSCRIPTION FACTOR P65 1.6 mM

sample_4: RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 1 1.6 mM; TRANSCRIPTION FACTOR P65, [U-99% 13C; U-99% 15N], 0.8 mM

sample_1: RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 1, [U-99% 13C; U-99% 15N], 0.8 mM; TRANSCRIPTION FACTOR P65 1.6 mM

sample_2: RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 1 1.6 mM; TRANSCRIPTION FACTOR P65, [U-99% 13C; U-99% 15N], 0.8 mM

sample_conditions_1: ionic strength: 0 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC ALIPHATICsample_3isotropicsample_conditions_1
2D 1H-13C HSQC AROMATICsample_3isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D 1H- 15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_3isotropicsample_conditions_1
3D INTERMOLECULAR NOESYsample_3isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
2D 1H-13C HSQC ALIPHATICsample_2isotropicsample_conditions_1
2D 1H-13C HSQC AROMATICsample_2isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D 1H- 15N NOESYsample_2isotropicsample_conditions_1
3D 1H-13C NOESYsample_4isotropicsample_conditions_1
3D INTERMOLECULAR NOESYsample_4isotropicsample_conditions_1

Software:

ARIA, Linge, O'Donoghue and Nilges - structure calculation

CNS, Brunger A. T. et.al. - refinement

CcpNMR, CCPN - chemical shift assignment, peak picking

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

VNMR, Varian - collection

YASARA, Krieger et al - refinement

NMR spectrometers:

  • VARIAN INOVA 600 MHz
  • Varian INOVA 800 MHz

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