BMRB Entry 26867

Name: HADDOCK model of the complex between the KIX domain of CBP and the transactivation domain of p65
Published: 2017-03-02

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PDB ID: 5u4k
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR26867
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

HADDOCK model of the complex between the KIX domain of CBP and the transactivation domain of p65

Deposition date:

2016-08-04

Original release date:

2017-03-02

Authors:

Lecoq, Lauriane; Raiola, L.; Cyr, N.; Chabot, P.; Arseneault, G.; Omichinski, J.

Citation:

Citation: Lecoq, Lauriane; Raiola, Luca; Chabot, Philippe; Cyr, Normand; Arseneault, Genevieve; Legault, Pascale; Omichinski, James. "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:
CREB-BINDING_PROTEIN, polymer, 87 residues, 10339.847 Da.
TRANSCRIPTION_FACTOR_P65, polymer, 33 residues, 3373.5739 Da.

Natural source:

Natural source: Common Name: Mouse Taxonomy ID: 10090 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Mus musculus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET21a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
CREB-BINDING_PROTEIN: GVRKGWHEHVTQDLRSHLVH KLVQAIFPTPDPAALKDRRM ENLVAYAKKVEGDMYESANS RDEYYHLLAEKIYKIQKELE EKRRSRL
TRANSCRIPTION_FACTOR_P65: GSPGYPNGLLSGDEDFSSIA DMDFSALLSQISS

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
- assigned_chem_shift_list_1_2

Data type	Count
13C chemical shifts	476
15N chemical shifts	118
1H chemical shifts	636

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	CREB-BINDING PROTEIN	1
2	TRANSCRIPTION FACTOR P65	2

Entities:

Entity 1, CREB-BINDING PROTEIN 87 residues - 10339.847 Da.

1

GLY

VAL

ARG

LYS

GLY

TRP

HIS

GLU

HIS

VAL

2

THR

GLN

ASP

LEU

ARG

SER

HIS

LEU

VAL

HIS

3

LYS

LEU

VAL

GLN

ALA

ILE

PHE

PRO

THR

PRO

4

ASP

PRO

ALA

LEU

LYS

ASP

ARG

MET

5

GLU

ASN

LEU

VAL

ALA

TYR

ALA

LYS

VAL

6

GLU

GLY

ASP

MET

TYR

GLU

SER

ALA

ASN

SER

7

ARG

ASP

GLU

TYR

HIS

LEU

ALA

GLU

8

LYS

ILE

TYR

LYS

ILE

GLN

LYS

GLU

LEU

GLU

9

GLU

LYS

ARG

SER

ARG

LEU

Entity 2, TRANSCRIPTION FACTOR P65 33 residues - 3373.5739 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_1: CREB-BINDING PROTEIN, [U-13C; U-15N], 0.8 mM; TRANSCRIPTION FACTOR P65 1.6 mM

sample_2: CREB-BINDING PROTEIN, [U-13C; U-15N], 0.8 mM; TRANSCRIPTION FACTOR P65 1.6 mM

sample_3: CREB-BINDING PROTEIN 1.4 mM; TRANSCRIPTION FACTOR P65, [U-13C; U-15N], 0.7 mM

sample_4: CREB-BINDING PROTEIN 1.4 mM; TRANSCRIPTION FACTOR P65, [U-13C; U-15N], 0.7 mM

sample_conditions_1: ionic strength: 0.0 mM; pH: 6.500; pressure: 1.000 atm; temperature: 300.000 K

Experiments:

Name	Sample	Sample state	Sample conditions
1H-15N HSQC	sample_1	solution	sample_conditions_1
HNCO	sample_1	solution	sample_conditions_1
HNCACB	sample_1	solution	sample_conditions_1
CCC-TOCSY	sample_1	solution	sample_conditions_1
HCC-TOCSY	sample_1	solution	sample_conditions_1
1H-13C HSQC	sample_2	solution	sample_conditions_1
HCCH-COSY	sample_2	solution	sample_conditions_1
Intermolecular NOESY	sample_2	solution	sample_conditions_1
1H-15N HSQC	sample_3	solution	sample_conditions_1
HNCO	sample_3	solution	sample_conditions_1
HNCACB	sample_3	solution	sample_conditions_1
HCCONH	sample_3	solution	sample_conditions_1
1H-13C HSQC	sample_4	solution	sample_conditions_1
Intermolecular NOESY	sample_4	solution	sample_conditions_1

Software:

AutoDep v4.3, PDBe - collection

CNS vany, Brunger, Adams, Clore, Gros, Nilges and Read - chemical shift assignment

CcpNmr vany, CCPN - chemical shift assignment

HADDOCK vany, Alexandre Bonvin - data analysis

NMRPIPE vany, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis

NMR spectrometers:

Varian UnityInova 600 MHz

UNP	CBP_MOUSE TF65_HUMAN
AlphaFold	E9QPH4 Q6SLK1