BMRB Entry 16859

Name: Solution structure of the double PHD (plant homeodomain) fingers of human transcriptional protein DPF3b bound to a histone N-terminal H3 peptide
Published: 2010-09-03

Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16859

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Nicholas Rego and David Koes
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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 N-terminal H3 peptide

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_N-terminal_H3, polymer, 20 residues, 2231.623 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: recombinant technology Host organism: Escherichia coli Vector: pGEX4T-1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
histone_N-terminal_H3: ARTKQTARKSTGGXAPRKQL
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	820

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	histone_N-terminal_H3	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_N-terminal_H3 20 residues - 2231.623 Da.

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

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

Name	Sample	Sample state	Sample conditions
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 NOEST	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HN(COCA)CB	sample_1	isotropic	sample_conditions_1

BMRB	16858 16858 16861 16865
PDB	1M1D 2KTB 2KWJ 3V43 4LLB 2KWJ 2KWK 2KWN 2KWO
GB	AET74057 AAX20019 EDL02734 EGV99590 EHH28015 EHH63746
DBJ	BAC30204
REF	NP_001254554 NP_001267471 XP_001140541 XP_001254780 XP_001375927
SP	P58269 Q92784
TPG	DAA25179
AlphaFold	P58269 Q92784

BMRB Entry 16859

Additional metadata:

Assembly:

Entities:

Samples:

Experiments:

Software:

NMR spectrometers:

Related Database Links:

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

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

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