BMRB Entry 30808

Name: Solution structure of the PHD1 domain of histone demethylase KDM5A
Published: 2021-03-01

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PDB ID: 7klo
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30808
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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 PHD1 domain of histone demethylase KDM5A

Deposition date:

2020-10-30

Original release date:

2021-03-01

Authors:

Longbotham, E.; Kelly, M.; Fujimori, D.

Citation:

Citation: Longbotham, J.; Kelly, M.; Fujimori, D.. "Recognition of Histone H3 Methylation States by the PHD1 Domain of Histone Demethylase KDM5A" ACS Chem. Biol. 18, 1915-1925 (2023).
PubMed: 33621062

Assembly members:

Assembly members:
entity_1, polymer, 59 residues, 6605.556 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 BL21(DE3)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GSVNFVDLYVCMFCGRGNNE DKLLLCDGCDDSYHTFCLIP PLPDVPKGDWRCPKCVAEE

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	202
15N chemical shifts	53
1H chemical shifts	380

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	2
3	unit_3	2

Entities:

Entity 1, unit_1 59 residues - 6605.556 Da.

1

GLY

SER

VAL

ASN

PHE

VAL

ASP

LEU

TYR

VAL

2

CYS

MET

PHE

CYS

GLY

ARG

GLY

ASN

GLU

3

ASP

LYS

LEU

CYS

ASP

GLY

CYS

ASP

4

ASP

SER

TYR

HIS

THR

PHE

CYS

LEU

ILE

PRO

5

PRO

LEU

PRO

ASP

VAL

PRO

LYS

GLY

ASP

TRP

6

ARG

CYS

PRO

LYS

CYS

VAL

ALA

GLU

Entity 2, unit_2 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: PHD1, [U-99% 13C; U-99% 15N], 900 uM; HEPES 50 mM; NaCl 150 mM; beta-mercaptoethanol 5 mM; ZnCl2 0.1 mM

sample_2: PHD1, [U-99% 13C; U-99% 15N], 550 uM; HEPES 50 mM; NaCl 150 mM; beta-mercaptoethanol 5 mM; ZnCl2 0.1 mM

sample_conditions_1: ionic strength: 150 mM; pH: 7.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
CBCACONH	sample_2	isotropic	sample_conditions_1
CBCANH	sample_2	isotropic	sample_conditions_1
3D (H)CCCONH-TOCSY	sample_1	isotropic	sample_conditions_1
3D H(CC)(CO)NH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D NOESY	sample_1	isotropic	sample_conditions_1
N HSQC	sample_1	isotropic	sample_conditions_1
C HSQC	sample_1	isotropic	sample_conditions_1

Software:

ARIA v2.3.2, Linge, O'Donoghue and Nilges - refinement, structure calculation

CcpNmr Analysis v2.4.2, CCPN - chemical shift assignment, peak picking

NMR spectrometers:

Bruker AVANCE 600 MHz

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