BMRB Entry 30243

Name: NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and the transactivation domain 1 of p65
Published: 2017-03-01

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PDB ID: 5urn
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30243
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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 the transactivation domain 1 of p65

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:

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).
PubMed: 28334776

Assembly members:

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

Entity Sequences (FASTA):

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

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	641
15N chemical shifts	152
1H chemical shifts	1019

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2	2

Entities:

Entity 1, entity_1 115 residues - 12903.701 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

Entity 2, entity_2 33 residues - 3378.591 Da.

1

GLY

SER

PRO

GLY

TYR

PRO

ASN

GLY

LEU

2

SER

GLY

ASP

GLU

ASP

PHE

SER

ILE

ALA

3

ASP

MET

ASP

PHE

SER

ALA

LEU

SER

GLN

4

ILE

SER

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:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC ALIPHATIC	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC AROMATIC	sample_3	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H- 15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_3	isotropic	sample_conditions_1
3D INTERMOLECULAR NOESY	sample_3	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC ALIPHATIC	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC AROMATIC	sample_2	isotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D 1H- 15N NOESY	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_4	isotropic	sample_conditions_1
3D INTERMOLECULAR NOESY	sample_4	isotropic	sample_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 HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks