BMRB Entry 30502

Name: Solution structure of ZZZ3 ZZ domain in complex with histone H3K4ac peptide
Published: 2018-09-12

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PDB ID: 6e86
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30502
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 ZZZ3 ZZ domain in complex with histone H3K4ac peptide

Deposition date:

2018-07-27

Original release date:

2018-09-12

Authors:

Zhang, Y.; Kutateladze, T.

Citation:

Citation: Mi, Wenyi; Zhang, Yi; Lyu, Jie; Wang, Xiaolu; Tong, Qiong; Peng, Danni; Xue, Yongming; Tencer, Adam; Wen, Hong; Li, Wei; Kutateladze, Tatiana; Shi, Xiaobing. "The ZZ-type zinc finger of ZZZ3 modulates the ATAC complex-mediated histone acetylation and gene activation." Nat. Commun. 9, 3759-3759 (2018).
PubMed: 30217978

Assembly members:

Assembly members:
entity_1, polymer, 64 residues, 7279.126 Da.
entity_2, polymer, 8 residues, 975.104 Da.
entity_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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GPLGSVQHVGFKCDNCGIEP IQGVRWHCQDCPPEMSLDFC DSCSDCLHETDIHKEDHQLE PIYR
entity_2: ARTXQTAR

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	194
15N chemical shifts	62
1H chemical shifts	409

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2	2
3	entity_ZN, 1	3
4	entity_ZN, 2	3

Entities:

Entity 1, entity_1 64 residues - 7279.126 Da.

1

GLY

PRO

LEU

GLY

SER

VAL

GLN

HIS

VAL

GLY

2

PHE

LYS

CYS

ASP

ASN

CYS

GLY

ILE

GLU

PRO

3

ILE

GLN

GLY

VAL

ARG

TRP

HIS

CYS

GLN

ASP

4

CYS

PRO

GLU

MET

SER

LEU

ASP

PHE

CYS

5

ASP

SER

CYS

SER

ASP

CYS

LEU

HIS

GLU

THR

6

ASP

ILE

HIS

LYS

GLU

ASP

HIS

GLN

LEU

GLU

7

PRO

ILE

TYR

ARG

Entity 2, entity_2 8 residues - 975.104 Da.

1

ALA

ARG

THR

ALY

GLN

THR

ALA

ARG

Entity 3, entity_ZN, 1 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: ZZ domain of ZZZ3, [U-13C; U-15N], 2 mM; H3K4ac 4 nM; NaCl 100 mM; D2O, [U-99% 2H], 7%

sample_conditions_1: ionic strength: 0.1 M; pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H TOCSY 13C/15N filtered	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D filtered 1H-13C NOESY	sample_1	isotropic	sample_conditions_1

Software:

VNMR, Varian - collection

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

Analysis, CCPN - chemical shift assignment

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

AMBER, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

NMR spectrometers:

Varian INOVA 900 MHz
Varian INOVA 600 MHz

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