BMRB Entry 27915

Name: NFkappaB p50DD homodimer
Published: 2019-11-08

Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR27915

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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: NFkappaB p50DD homodimer PubMed: 31587407

Deposition date: 2019-05-16 Original release date: 2019-11-08

Authors: Kohl, Bastian; Granitzka, Vanessa; Singh, Amrinder; Quintas, Pedro; Xiromeriti, Elli; Mortel, Fabian; Xiromeriti, Elli; Wright, Peter; Dyson, Jane; Stoll, Raphael

Citation: Kohl, Bastian; Granitzka, Vanessa; Singh, Amrinder; Quintas, Pedro; Xiromeriti, Elli; Mortel, Fabian; Kroon, Gerard; Wright, Peter; Dyson, Jane; Stoll, Raphael. "Comparison of backbone dynamics of the p50 dimerization domain of NFkB in the homodimeric transcription factor NFkB1 and in its heterodimeric complex with RelA (p65)" Protein Sci. 28, 2064-2072 (2019).

Assembly members:
p50_homodimer, polymer, 121 residues, Formula weight is not available

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

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET-45b(+)

Entity Sequences (FASTA):
p50_homodimer: VGTGSNDDDDKAPNASNLKI VRMDRTAGCVTGGEEIYLLC DKVQKDDIQIRFYEEEENGG VWEGFGDFSPTDVHRQFAIV FKTPKYKDVNITKPASVFVQ LRRKSDLETSEPKPFLYYPE I

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
heteronucl_NOEs
- heteronuclear_noe_list_1
heteronucl_T1_relaxation
- heteronuclear_T1_list_1
heteronucl_T2_relaxation
- heteronuclear_T2_list_1

Data type	Count
13C chemical shifts	221
15N chemical shifts	110
1H chemical shifts	110
T1 relaxation values	90
T2 relaxation values	90
heteronuclear NOE values	86

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	p50 DD, 1	1
2	p50 DD, 2	1

Entities:

Entity 1, p50 DD, 1 121 residues - Formula weight is not available

residues 233-353 of mouse p50

1

VAL

GLY

THR

GLY

SER

ASN

ASP

2

LYS

ALA

PRO

ASN

ALA

SER

ASN

LEU

LYS

ILE

3

VAL

ARG

MET

ASP

ARG

THR

ALA

GLY

CYS

VAL

4

THR

GLY

GLU

ILE

TYR

LEU

CYS

5

ASP

LYS

VAL

GLN

LYS

ASP

ILE

GLN

ILE

6

ARG

PHE

TYR

GLU

ASN

GLY

7

VAL

TRP

GLU

GLY

PHE

GLY

ASP

PHE

SER

PRO

8

THR

ASP

VAL

HIS

ARG

GLN

PHE

ALA

ILE

VAL

9

PHE

LYS

THR

PRO

LYS

TYR

LYS

ASP

VAL

ASN

10

ILE

THR

LYS

PRO

ALA

SER

VAL

PHE

VAL

GLN

11

LEU

ARG

LYS

SER

ASP

LEU

GLU

THR

SER

12

GLU

PRO

LYS

PRO

PHE

LEU

TYR

PRO

GLU

13

ILE

Samples:

sample_1: p50 homodimer, [U-13C; U-15N; U-2H], 1.5 mM; HEPES 50 mM; DTT 150 mM

sample_conditions_1: ionic strength: 0 M; pH: 6.8; 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-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HN(COCA)CB	sample_1	isotropic	sample_conditions_1
T1, T2, NOE	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1

Software:

NMRView vJ, Johnson, One Moon Scientific - chemical shift assignment

CCPNMR v2.7, CCPN - chemical shift assignment

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

TOPSPIN v3.5, Bruker Biospin - data analysis

NMR spectrometers:

Bruker DRX 600 MHz
Bruker Avance 700 MHz
Bruker Avance 800 MHz

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