BMRB Entry 16865

Name: Solution structure of the double PHD (plant homeodomain) fingers of human transcriptional protein DPF3b bound to a histone H4 peptide containing N-terminal acetylation at serine 1
Published: 2010-09-03

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PDB ID: 2kwo
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16865
MolProbity Validation Chart

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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 N-terminal acetylation at serine 1

Deposition date:

2010-04-14

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_serine_1, polymer, 20 residues, 1914.308 Da.
double_PHD_fingers, polymer, 114 residues, 12746.515 Da.
ACS, non-polymer, 395.452 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_serine_1: XGRGKGGKGLGKGGAKRHRK
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	801

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	histone_H4_acet_serine_1	1
2	double_PHD_fingerss	2
3	ACS	3
4	ZINC ION_1	4
5	ZINC ION_2	4
6	ZINC ION_3	4
7	ZINC ION_4	4

Entities:

Entity 1, histone_H4_acet_serine_1 20 residues - 1914.308 Da.

1		SAC	GLY	ARG	GLY	LYS	GLY	GLY	LYS	GLY	LEU
2		GLY	LYS	GLY	GLY	ALA	LYS	ARG	HIS	ARG	LYS

Entity 2, double_PHD_fingerss 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, ACS - C13 H21 N3 O7 S2 - 395.452 Da.

1

ACS

Entity 4, ZINC ION_1 - Zn - 65.409 Da.

1

ZN

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

Related Database Links:

PDB	1EQZ 1F66 1HQ3 1ID3 1KX3 1KX4 1KX5 1M18 1M19 1M1A 1P34 1P3A 1P3B 1P3F 1P3G 1P3I 1P3K 1P3L 1P3M 1P3O 1P3P 1S32 1TZY 1U35 1ZBB 1ZLA 2ARO 2CV5 2F8N 2FJ7 2HIO 2IO5 2KWO 2NQB 2NZD 2PYO 2YFW 3A6N 3AFA 3AN2 3AV1 3AV2 3AYW 3AZE 3AZF 3AZG 3AZH 3AZI 3AZJ 3AZK 3AZL 3AZM 3AZN 3B6F 3B6G 3C1C 3C9K 3KUY 3KXB 3LEL 3LJA 3LZ0 3LZ1 3MGP 3MGQ 3MGR 3MGS 3MNN 3MVD 3NQU 3O62 3R45 3REH 3REI 3REJ 3REK 3REL 3TU4 3UT9 3UTA 3UTB 3W96 3W97 3W98 3WA9 3WAA 3WKJ 3WTP 3X1S 3X1T 3X1U 3X1V 4GQB 4H9N 4H9O 4H9P 4H9Q 4H9R 4HGA 4J8U 4J8V 4J8W 4J8X 4JJN 4KGC 4KUD 4LD9 4M38 4PSX 4QLC 4R8P 4UUZ 4WU8 4WU9 5BNV 5BNX 5BO0 5BS7 5BSA 5C3I 2KWJ 2KWK 2KWN 2KWO
DBJ	BAA19208 BAA21442 BAA85120 BAB08365 BAB09507 BAC30204
EMBL	CAA17818 CAA24130 CAA24373 CAA24645 CAA24924
GB	AAA20820 AAA20821 AAA28606 AAA30002 AAA30024 AAX20019 EDL02734 EGV99590 EHH28015 EHH63746
PIR	D56618 S11312 S21367 S68537
PRF	0901261A 0912198A 1202262E 1314298A 1707275C
REF	NP_001011609 NP_001016869 NP_001027284 NP_001027288 NP_001027293 NP_001254554 NP_001267471 XP_001140541 XP_001254780 XP_001375927
SP	P02309 P04914 P04915 P08436 P09322 P58269 Q92784
TPE	CBF86829 CBF88885 CEL65759 CEL73296
TPG	DAA07130 DAA10515 DAA13862 DAA16108 DAA16158 DAA25179
BMRB	16858 16859 16861
AlphaFold	P02309 P04914 P04915 P08436 P09322 P58269 Q92784

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

BMRB Entry 16865

Additional metadata:

Assembly:

Entities:

Samples:

Experiments:

Software:

NMR spectrometers:

Related Database Links:

1		SAC	GLY	ARG	GLY	LYS	GLY	GLY	LYS	GLY	LEU
2		GLY	LYS	GLY	GLY	ALA	LYS	ARG	HIS	ARG	LYS

1		SAC	GLY	ARG	GLY	LYS	GLY	GLY	LYS	GLY	LEU
2		GLY	LYS	GLY	GLY	ALA	LYS	ARG	HIS	ARG	LYS

1		SAC	GLY	ARG	GLY	LYS	GLY	GLY	LYS	GLY	LEU
2		GLY	LYS	GLY	GLY	ALA	LYS	ARG	HIS	ARG	LYS