BMRB Entry 18842
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18842
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Title: NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and Rad4 PubMed: 23295669
Deposition date: 2012-11-16 Original release date: 2013-01-22
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
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 552 |
| 15N chemical shifts | 144 |
| 1H chemical shifts | 862 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | Tfb1 | 1 |
| 2 | Rad4 | 2 |
Entities:
Entity 1, Tfb1 119 residues - 12903.807 Da.
| 1 | PRO | SER | HIS | SER | GLY | ALA | ALA | ILE | PHE | GLU | ||||
| 2 | LYS | VAL | SER | GLY | ILE | ILE | ALA | ILE | ASN | GLU | ||||
| 3 | ASP | VAL | SER | PRO | ALA | GLU | LEU | THR | TRP | ARG | ||||
| 4 | SER | THR | ASP | GLY | ASP | LYS | VAL | HIS | THR | VAL | ||||
| 5 | VAL | LEU | SER | THR | ILE | ASP | LYS | LEU | GLN | ALA | ||||
| 6 | THR | PRO | ALA | SER | SER | GLU | LYS | MET | MET | LEU | ||||
| 7 | ARG | LEU | ILE | GLY | LYS | VAL | ASP | GLU | SER | LYS | ||||
| 8 | LYS | ARG | LYS | ASP | ASN | GLU | GLY | ASN | GLU | VAL | ||||
| 9 | VAL | PRO | LYS | PRO | GLN | ARG | HIS | MET | PHE | SER | ||||
| 10 | PHE | ASN | ASN | ARG | THR | VAL | MET | ASP | ASN | ILE | ||||
| 11 | LYS | MET | THR | LEU | GLN | GLN | ILE | ILE | SER | ARG | ||||
| 12 | TYR | LYS | ASP | ALA | ASP | GLY | ASN | SER | SER |
Entity 2, Rad4 42 residues - 1747.696 Da.
| 1 | GLY | SER | THR | ASP | ASP | SER | VAL | GLU | GLU | ILE | ||||
| 2 | GLN | SER | SER | GLU | GLU | ASP | TYR | ASP | SER | GLU | ||||
| 3 | GLU | PHE | GLU | ASP | VAL | THR | ASP | GLY | ASN | GLU | ||||
| 4 | VAL | ALA | GLY | VAL | GLU | ASP | ILE | SER | VAL | GLU | ||||
| 5 | ILE | LYS |
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:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_3 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_6 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_5 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_4 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_4 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_4 | isotropic | sample_conditions_1 |
| 3D H(CCO)NH | sample_4 | isotropic | sample_conditions_1 |
| 3D HCCH-COSY | sample_5 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_6 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_5 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_2 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D H(CCO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-COSY | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_3 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_2 | isotropic | sample_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 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts