BMRB Entry 51161

Name: Backbone assignments of p65 DNA binding domain in complex with DNA.
Published: 2021-11-04

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR51161

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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: Backbone assignments of p65 DNA binding domain in complex with DNA. PubMed: 35171557

Deposition date: 2021-10-29 Original release date: 2021-11-04

Authors: Singh, Amrinder; Martinez-Yamout, Maria; Wright, Peter; Dyson, Jane

Citation: Singh, Amrinder; Martinez-Yamout, Maria; Wright, Peter; Dyson, Jane. "Interactions of a Long Noncoding RNA with Domains of NF-kB and IkBa: Implications for the Inhibition of Non-Signal-Related Phosphorylation" Biochemistry 61, 367-376 (2022).

Assembly members:
entity_1, polymer, 173 residues, Formula weight is not available
entity_2, polymer, 18 residues, Formula weight is not available

Natural source: Common Name: E. coli Taxonomy ID: 562 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET22b

Entity Sequences (FASTA):
entity_1: AYVEIIEQPKQRGMRFRYKC EGRSAGSIPGERSTDTTKTH PTIKINGYTGPGTVRISLVT KDPPHRPHPHELVGKDCRDG YYEADLCPDRSIHSFQNLGI QCVKKRDLEQAISQRIQTNN NPFHVPIEEQRGDYDLNAVR LCFQVTVRDPAGRPLLLTPV LSHPIFDNRAPNT
entity_2: ATCTGGGAATTCCCAGAT

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
15N chemical shifts	134
1H chemical shifts	134

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	p65 DBD	1
2	DNA chain 1	2
3	DNA chain 2	2

Entities:

Entity 1, p65 DBD 173 residues - Formula weight is not available

The sequence starts from 19.

1

ALA

TYR

VAL

GLU

ILE

GLU

GLN

PRO

LYS

2

GLN

ARG

GLY

MET

ARG

PHE

ARG

TYR

LYS

CYS

3

GLU

GLY

ARG

SER

ALA

GLY

SER

ILE

PRO

GLY

4

GLU

ARG

SER

THR

ASP

THR

LYS

THR

HIS

5

PRO

THR

ILE

LYS

ILE

ASN

GLY

TYR

THR

GLY

6

PRO

GLY

THR

VAL

ARG

ILE

SER

LEU

VAL

THR

7

LYS

ASP

PRO

HIS

ARG

PRO

HIS

PRO

HIS

8

GLU

LEU

VAL

GLY

LYS

ASP

CYS

ARG

ASP

GLY

9

TYR

GLU

ALA

ASP

LEU

CYS

PRO

ASP

ARG

10

SER

ILE

HIS

SER

PHE

GLN

ASN

LEU

GLY

ILE

11

GLN

CYS

VAL

LYS

ARG

ASP

LEU

GLU

GLN

12

ALA

ILE

SER

GLN

ARG

ILE

GLN

THR

ASN

13

ASN

PRO

PHE

HIS

VAL

PRO

ILE

GLU

GLN

14

ARG

GLY

ASP

TYR

ASP

LEU

ASN

ALA

VAL

ARG

15

LEU

CYS

PHE

GLN

VAL

THR

VAL

ARG

ASP

PRO

16

ALA

GLY

ARG

PRO

LEU

THR

PRO

VAL

17

LEU

SER

HIS

PRO

ILE

PHE

ASP

ASN

ARG

ALA

18

PRO

ASN

THR

Entity 2, DNA chain 1 18 residues - Formula weight is not available

1

DA

DT

DC

DT

DG

DA

DT

2

DT

DC

DA

DG

DA

DT

Samples:

sample_1: p65DBD, [U-13C; U-15N; U-2H], 350 uM; DNA 350 uM; NaCl 150 mM

sample_conditions_1: ionic strength: 0.150 M; pH: 6.8; temperature: 300 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CACB	sample_1	isotropic	sample_conditions_1

Software:

CcpNMR - chemical shift assignment

NMR spectrometers:

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