BMRB Entry 18842

Name: NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and Rad4
Published: 2013-01-22

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PDB ID: 2m14
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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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and Rad4

Deposition date:

2012-11-16

Original release date:

2013-01-22

Authors:

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

Citation:

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).
PubMed: 23295669

Assembly members:

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

Natural source:

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

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pGEX-2TK

Entity Sequences (FASTA):

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

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	552
15N chemical shifts	144
1H chemical shifts	862

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

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

ILE

PHE

GLU

2

LYS

VAL

SER

GLY

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

GLU

LYS

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

ARG

THR

VAL

MET

ASP

ASN

ILE

11

LYS

MET

THR

LEU

GLN

ILE

SER

ARG

12

TYR

LYS

ASP

ALA

ASP

GLY

ASN

SER

Entity 2, Rad4 42 residues - 1747.696 Da.

1

GLY

SER

THR

ASP

SER

VAL

GLU

ILE

2

GLN

SER

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

BMRB	18229 19791 25540
PDB	1Y5O 2GS0 2K2U 2L2I 2LOX 2M14 2MKR 2N0Y 2M14
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
AlphaFold	P32776 P14736