BMRB Entry 16694

Name: Solution Structure of the Second Bromodomain of Human Polybromo in complex with an acetylated peptide from Histone 3
Published: 2010-05-05

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PDB ID: 2ktb
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16694
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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:

Solution Structure of the Second Bromodomain of Human Polybromo in complex with an acetylated peptide from Histone 3

Deposition date:

2010-01-27

Original release date:

2010-05-05

Authors:

Charlop-Powers, Zachary; Zhang, Qiang; Zeng, Lei

Citation:

Citation: Charlop-Powers, Zachary; Zeng, Lei; Zhang, Qiang; Zhou, Ming-Ming. "Structural insights into selective histone H3 recognition by the human Polybromo bromodomain 2." Cell Res. 20, 529-538 (2010).
PubMed: 20368734

Assembly members:

Assembly members:
H3_Peptide, polymer, 20 residues, 2061.412 Da.
Polybromo_Bromdomain2, polymer, 121 residues, 13676.851 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: obtained from a vendor

Entity Sequences (FASTA):

Entity Sequences (FASTA):
H3_Peptide: ARTKQTARKSTGGKAPRKQL
Polybromo_Bromdomain2: STEGSSPAYLKEILEQLLEA IVVATNPSGRLISELFQKLP SKVQYPDYYAIIKEPIDLKT IAQRIQNGSYKSIHAMAKDI DLLAKNAKTYNEPGSQVFKD ANSIKKIFYMKKAEIEHHEM A

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	379
15N chemical shifts	113
1H chemical shifts	844

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	H3_Peptide	1
2	Polybromo_Bromdomain2	2

Entities:

Entity 1, H3_Peptide 20 residues - 2061.412 Da.

1		ALA	ARG	THR	LYS	GLN	THR	ALA	ARG	LYS	SER
2		THR	GLY	GLY	LYS	ALA	PRO	ARG	LYS	GLN	LEU

Entity 2, Polybromo_Bromdomain2 121 residues - 13676.851 Da.

1

SER

THR

GLU

GLY

SER

PRO

ALA

TYR

LEU

2

LYS

GLU

ILE

LEU

GLU

GLN

LEU

GLU

ALA

3

ILE

VAL

ALA

THR

ASN

PRO

SER

GLY

ARG

4

LEU

ILE

SER

GLU

LEU

PHE

GLN

LYS

LEU

PRO

5

SER

LYS

VAL

GLN

TYR

PRO

ASP

TYR

ALA

6

ILE

LYS

GLU

PRO

ILE

ASP

LEU

LYS

THR

7

ILE

ALA

GLN

ARG

ILE

GLN

ASN

GLY

SER

TYR

8

LYS

SER

ILE

HIS

ALA

MET

ALA

LYS

ASP

ILE

9

ASP

LEU

ALA

LYS

ASN

ALA

LYS

THR

TYR

10

ASN

GLU

PRO

GLY

SER

GLN

VAL

PHE

LYS

ASP

11

ALA

ASN

SER

ILE

LYS

ILE

PHE

TYR

MET

12

LYS

ALA

GLU

ILE

GLU

HIS

GLU

MET

13

ALA

Samples:

sample_3: Polybromo Bromdomain2, [U-100% 13C; U-100% 15N], 0.8 mM; H3 Peptide 8 mM; D2O 100%

sample_1: Polybromo Bromdomain2, [U-100% 15N], 0.5 mM; H3 Peptide 2.5 mM; H2O 90%; D2O 10%

sample_2: Polybromo Bromdomain2, [U-100% 13C; U-100% 15N], 0.5 mM; H3 Peptide 2.5 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.1 M; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 1H-13C NOESY	sample_3	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D HN(CO)CA	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1

Software:

ARIA v2.2, Linge, O'Donoghue and Nilges - structure solution

CNS v2.2, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

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

NMRView, Johnson, One Moon Scientific - chemical shift assignment

NMR spectrometers:

Bruker DRX 500 MHz
Bruker Avance 800 MHz

Related Database Links:

BMRB	18385
PDB	1EQZ 1F66 1HQ3 1ID3 1KX3 1KX4 1KX5 1M18 1M19 1M1A 1P34 1P3A 1P3B 1P3F 1P3G 1P3I 1P3K 1P3L 1P3M 1P3O 1P3P 1PU9 1S32 1TZY 1U35 1ZBB 1ZLA 2ARO 2CV5 2F8N 2FJ7 2HIO 2IO5 2KFT 2KWK 2NQB 2NZD 2PYO 2YBA 3A1B 3A6N 3AFA 3AV1 3AV2 3AYW 3AZE 3AZF 3AZG 3AZH 3AZI 3AZJ 3AZK 3AZL 3AZM 3AZN 3B6F 3B6G 3C1B 3C1C 3C9K 3KUY 3KXB 3LEL 3LJA 3LZ0 3LZ1 3MGP 3MGQ 3MGR 3MGS 3MNN 3MVD 3O62 3REH 3REI 3REJ 3REK 3REL 3TU4 3UT9 3UTA 3UTB 3W96 3W97 3W99 3WA9 3WAA 3WKJ 3WTP 3X1S 3X1T 3X1U 3X1V 4H9N 4H9O 4H9P 4H9Q 4H9R 4H9S 4HGA 4J8U 4J8V 4J8W 4J8X 4JJN 4KGC 4KUD 4LD9 4LK9 4QLC 4R8P 4UUZ 4WU8 4WU9 5C3I 2KTB 3HMF 3LJW
DBJ	BAA20144 BAA21441 BAA31218 BAA81840 BAA81841
EMBL	CAA17819 CAA23780 CAA24375 CAA24647 CAA24952
GB	AAA19824 AAA29441 AAA29965 AAA30003 AAA30026
PIR	A56580 A56618 A56654 I37460 I48113
PRF	0710252A 0806228A 1202262D 1202289A 1303352A
REF	NP_001005101 NP_001005464 NP_001013074 NP_001013721 NP_001014411 XP_008563175
SP	A1CP80 A1D240 A2QRR5 A2XHJ3 A2Y533
TPE	CBF88887 CEL66806 CEL70515 CEL74279 CEL78184
TPG	DAA07131 DAA10514 DAA16173 DAA16175 DAA16178
UNP	Q86U86
AlphaFold	Q9H314 A1CP80 A2Y533 A2XHJ3 A2QRR5 A1D240

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

1		ALA	ARG	THR	LYS	GLN	THR	ALA	ARG	LYS	SER
2		THR	GLY	GLY	LYS	ALA	PRO	ARG	LYS	GLN	LEU

1		ALA	ARG	THR	LYS	GLN	THR	ALA	ARG	LYS	SER
2		THR	GLY	GLY	LYS	ALA	PRO	ARG	LYS	GLN	LEU

1		ALA	ARG	THR	LYS	GLN	THR	ALA	ARG	LYS	SER
2		THR	GLY	GLY	LYS	ALA	PRO	ARG	LYS	GLN	LEU