BMRB Entry 17244

Name: Structural basis for histone code recognition by BRPF2-PHD1 finger
Published: 2012-07-25

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PDB ID: 2l43
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR17244
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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:

Structural basis for histone code recognition by BRPF2-PHD1 finger

Deposition date:

2010-10-10

Original release date:

2012-07-25

Authors:

Qin, Su; Zhang, Jiahai; Wu, Jihui; Shi, Yunyu

Citation:

Citation: Liu, Lei; Qin, Su; Zhang, Jiahai; Ji, Peng; Shi, Yunyu; Wu, Jihui. "Solution structure of an atypical PHD finger in BRPF2 and its interaction with DNA." J. Struct. Biol. 180, 165-173 (2012).
PubMed: 22820306

Assembly members:

Assembly members:
BRPF2-PHD1, polymer, 88 residues, 8719.837 Da.
ZN, non-polymer, 65.409 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: recombinant technology Host organism: Escherichia coli Vector: pET22b(+)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
BRPF2-PHD1: ARTKQTARKSTGGSSGSSQS LIDEDAVCSICMDGESQNSN VILFCDMCNLAVHQECYGVP YIPEGQWLCRHCLQSRARPA LEHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	206
15N chemical shifts	82
1H chemical shifts	426

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	BRPF2-PHD1	1
2	Zinc 1	2
3	Zinc 2	2

Entities:

Entity 1, BRPF2-PHD1 88 residues - 8719.837 Da.

Histone H3(1-12) fused to the N-ternimal of BRPF2-PHD1 finger, linked by GSSGSS

1

ALA

ARG

THR

LYS

GLN

THR

ALA

ARG

LYS

SER

2

THR

GLY

SER

GLY

SER

GLN

SER

3

LEU

ILE

ASP

GLU

ASP

ALA

VAL

CYS

SER

ILE

4

CYS

MET

ASP

GLY

GLU

SER

GLN

ASN

SER

ASN

5

VAL

ILE

LEU

PHE

CYS

ASP

MET

CYS

ASN

LEU

6

ALA

VAL

HIS

GLN

GLU

CYS

TYR

GLY

VAL

PRO

7

TYR

ILE

PRO

GLU

GLY

GLN

TRP

LEU

CYS

ARG

8

HIS

CYS

LEU

GLN

SER

ARG

ALA

ARG

PRO

ALA

9

LEU

GLU

HIS

Entity 2, Zinc 1 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: BRPF2-PHD1, [U-100% 13C; U-100% 15N], 0.8 mM; ZINC ION 1.6 mM; Bis-Tris 20 mM; sodium chloride 150 mM; H2O 90%; D2O 10%

sample_2: BRPF2-PHD1, [U-100% 13C; U-100% 15N], 0.8 mM; ZINC ION 1.6 mM; Bis-Tris 20 mM; sodium chloride 150 mM; D2O 100%

sample_conditions_1: ionic strength: 0.15 M; pH: 6.7; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_1

Software:

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

SPARKY v3, Goddard - chemical shift assignment, data analysis, peak picking

TALOS, Cornilescu, Delaglio and Bax - chemical shift calculation, data analysis

ProcheckNMR, Laskowski and MacArthur - data analysis

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - refinement, structure solution

Molmol, Koradi, Billeter and Wuthrich - data analysis

NMR spectrometers:

Bruker DMX 500 MHz

GB	NP_055392 NP_003484
BMRB	16721
PDB	2KU3 2L43
REF	XP_009232775 XP_009232776 XP_009232777 XP_009232778 XP_009232779