BMRB Entry 16861

Name: Solution structure of the double PHD (plant homeodomain) fingers of human transcriptional protein DPF3b bound to a histone H4 peptide containing acetylation at lysine 16
Published: 2010-09-03

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PDB ID: 2kwn
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16861
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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 double PHD (plant homeodomain) fingers of human transcriptional protein DPF3b bound to a histone H4 peptide containing acetylation at lysine 16

Deposition date:

2010-04-13

Original release date:

2010-09-03

Authors:

Zeng, Lei; Zhang, Qiang; Li, SiDe; Plotnikov, Alexander; Walsh, Martin; ZHOU, MING-MING

Citation:

Citation: Zeng, Lei; Zhang, Qiang; Li, SiDe; Plotnikov, Alexander; Walsh, Martin; ZHOU, MING-MING. "Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b" Nature 466, 258-262 (2010).
PubMed: 20613843

Assembly members:

Assembly members:
histone_H4_acet_lys_16, polymer, 15 residues, 1681.058 Da.
double_PHD_fingers, polymer, 114 residues, 12746.515 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: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
histone_H4_acet_lys_16: GLGKGGAXRHRKVLR
double_PHD_fingers: GSYCDFCLGGSNMNKKSGRP EELVSCADCGRSGHPTCLQF TLNMTEAVKTYKWQCIECKS CILCGTSENDDQLLFCDDCD RGYHMYCLNPPVAEPPEGSW SCHLCWELLKEKAS

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	364
15N chemical shifts	117
1H chemical shifts	798

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	histone_H4_acet_lys_16	1
2	double_PHD_fingers	2
3	ZINC ION_1	3
4	ZINC ION_2	3
5	ZINC ION_3	3
6	ZINC ION_4	3

Entities:

Entity 1, histone_H4_acet_lys_16 15 residues - 1681.058 Da.

1

GLY

LEU

GLY

LYS

GLY

ALA

ALY

ARG

HIS

2

ARG

LYS

VAL

LEU

ARG

Entity 2, double_PHD_fingers 114 residues - 12746.515 Da.

1

GLY

SER

TYR

CYS

ASP

PHE

CYS

LEU

GLY

2

SER

ASN

MET

ASN

LYS

SER

GLY

ARG

PRO

3

GLU

LEU

VAL

SER

CYS

ALA

ASP

CYS

GLY

4

ARG

SER

GLY

HIS

PRO

THR

CYS

LEU

GLN

PHE

5

THR

LEU

ASN

MET

THR

GLU

ALA

VAL

LYS

THR

6

TYR

LYS

TRP

GLN

CYS

ILE

GLU

CYS

LYS

SER

7

CYS

ILE

LEU

CYS

GLY

THR

SER

GLU

ASN

ASP

8

ASP

GLN

LEU

PHE

CYS

ASP

CYS

ASP

9

ARG

GLY

TYR

HIS

MET

TYR

CYS

LEU

ASN

PRO

10

PRO

VAL

ALA

GLU

PRO

GLU

GLY

SER

TRP

11

SER

CYS

HIS

LEU

CYS

TRP

GLU

LEU

LYS

12

GLU

LYS

ALA

SER

Entity 3, ZINC ION_1 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: sodium phosphate 100 mM; DTT 2 mM; D2O 100%

sample_2: sodium phosphate 100 mM; DTT 2 mM; H2O 90%; D2O 10%

sample_conditions_1: 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(COCA)CB	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D_13C-Edited_13C/15N-filtered NOESY	sample_1	isotropic	sample_conditions_1

Software:

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

NMRPipe v2.3, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - chemical shift calculation, processing

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

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

NMR spectrometers:

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

BMRB	16858 16859 16865
PDB	2KWJ 2KWK 2KWN 2KWO
DBJ	BAC30204
GB	AAX20019 EDL02734 EGV99590 EHH28015 EHH63746
REF	NP_001254554 NP_001267471 XP_001140541 XP_001254780 XP_001375927
SP	P58269 Q92784
TPG	DAA25179
AlphaFold	Q6NWP7 P58269 Q92784