BMRB Entry 18439

Name: solution structures of BRD4 second bromodomain with NF-kB-K310ac peptide
Published: 2012-06-05

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PDB ID: 2lsp
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18439
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

solution structures of BRD4 second bromodomain with NF-kB-K310ac peptide

Deposition date:

2012-05-03

Original release date:

2012-06-05

Authors:

Zhang, Guangtao; Liu, Ruijie; Zhong, Yifei; Plotnikov, Alexander; Zhang, Weijia; Rusinova, Elena; Gerona-Nevarro, Guillermo; Moshkina, Natasha; Joshua, Jennifer; Chuang, Peter; Ohlmeyer, Michael; He, John Cijiang

Citation:

Citation: Zhang, Guangtao; Liu, Ruijie; Zhong, Yifei; Plotnikov, Alexander; Zhang, Weijia; Zeng, Lei; Rusinova, Elena; Gerona-Nevarro, Guillermo; Moshkina, Natasha; Joshua, Jennifer; Chuang, Peter; Ohlmeyer, Michael; He, John Cijiang; Zhou, Ming-Ming. "Down-regulation of NF-B transcriptional activity in HIV-associated kidney disease by BRD4 inhibition." J. Biol. Chem. 287, 28840-28851 (2012).
PubMed: 22645123

Assembly members:

Assembly members:
entity_1, polymer, 13 residues, 1663.968 Da.
entity_2, polymer, 128 residues, 14842.159 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: RTYETFXSIMKKS
entity_2: KDVPDSQQHPAPEKSSKVSE QLKCCSGILKEMFAKKHAAY AWPFYKPVDVEALGLHDYCD IIKHPMDMSTIKSKLEAREY RDAQEFGADVRLMFSNCYKY NPPDHEVVAMARKLQDVFEM RFAKMPDE

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	444
15N chemical shifts	117
1H chemical shifts	874

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	NF-kB-K310ac peptide	1
2	BRD4 second bromodomain	2

Entities:

Entity 1, NF-kB-K310ac peptide 13 residues - 1663.968 Da.

1

ARG

THR

TYR

GLU

THR

PHE

ALY

SER

ILE

MET

2

LYS

SER

Entity 2, BRD4 second bromodomain 128 residues - 14842.159 Da.

1

LYS

ASP

VAL

PRO

ASP

SER

GLN

HIS

PRO

2

ALA

PRO

GLU

LYS

SER

LYS

VAL

SER

GLU

3

GLN

LEU

LYS

CYS

SER

GLY

ILE

LEU

LYS

4

GLU

MET

PHE

ALA

LYS

HIS

ALA

TYR

5

ALA

TRP

PRO

PHE

TYR

LYS

PRO

VAL

ASP

VAL

6

GLU

ALA

LEU

GLY

LEU

HIS

ASP

TYR

CYS

ASP

7

ILE

LYS

HIS

PRO

MET

ASP

MET

SER

THR

8

ILE

LYS

SER

LYS

LEU

GLU

ALA

ARG

GLU

TYR

9

ARG

ASP

ALA

GLN

GLU

PHE

GLY

ALA

ASP

VAL

10

ARG

LEU

MET

PHE

SER

ASN

CYS

TYR

LYS

TYR

11

ASN

PRO

ASP

HIS

GLU

VAL

ALA

MET

12

ALA

ARG

LYS

LEU

GLN

ASP

VAL

PHE

GLU

MET

13

ARG

PHE

ALA

LYS

MET

PRO

ASP

GLU

Samples:

sample_2: sodium phosphate 100 mM; DTT, [U-100% 2H], 5 mM; D2O 10%; H2O 90%

sample_1: sodium phosphate 100 mM; DTT, [U-100% 2H], 5 mM; D2O 100%

sample_conditions_1: ionic strength: 100 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D HN(CO)CACB	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
3D 13C-Edited-15N/13C filtered NOESY	sample_1	isotropic	sample_conditions_1

Software:

ARIA v2.3, Linge, O'Donoghue and Nilges - refinement

NMRPipe v7.1, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - chemical shift calculation, processing

TALOS v3.70F1, Cornilescu, Delaglio and Bax - geometry optimization

NMRView v5.04, Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking

CNS v1.21, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

NMR spectrometers:

Bruker Avance 800 MHz
Bruker Avance 900 MHz
Bruker Avance 600 MHz
Bruker DRX 500 MHz

BMRB	15057 19738
PDB	2I8N 2LSP 2MJV 2OUO 2YEM 3JVL 3JVM 4KV4
REF	XP_004761195 XP_006524755 XP_006524756 XP_008763395
AlphaFold	Q6SLK1