6H8P

JMJD2A/ KDM4A COMPLEXED WITH NI(II), NOG AND Histone H1.4(18-32)K26me3 peptide (15-mer)

PDB DOI: https://doi.org/10.2210/pdb6H8P/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-08-03 Released: 2018-08-15
Deposition Author(s): Chowdhury, R., Walport, L.J., Schofield, C.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.212
R-Value Work: 0.192
R-Value Observed: 0.193

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Mechanistic and structural studies of KDM-catalysed demethylation of histone 1 isotype 4 at lysine 26.

Walport, L.J., Hopkinson, R.J., Chowdhury, R., Zhang, Y., Bonnici, J., Schiller, R., Kawamura, A., Schofield, C.J.

(2018) FEBS Lett 592: 3264-3273

PubMed: 30156264 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/1873-3468.13231
Primary Citation of Related Structures:
6H8P

PubMed Abstract:
N-Methylation of lysyl residues is widely observed on histone proteins. Using isolated enzymes, we report mechanistic and structural studies on histone lysine demethylase (KDM)-catalysed demethylation of N ^ε -methylated lysine 26 on histone 1 isotype 4 (H1.4). The results reveal that methylated H1.4K26 is a substrate for all members of the KDM4 subfamily and that KDM4A-catalysed demethylation of H1.4K26me3 peptide is similarly efficient to that of H3K9me3. Crystallographic studies of an H1.4K26me3:KDM4A complex reveal a conserved binding geometry to that of H3K9me3. In the light of the high activity of the KDM4s on this mark, our results suggest JmjC KDM-catalysed demethylation of H1.4K26 may be as prevalent as demethylation on the H3 tail and warrants further investigation in cells.

Organizational Affiliation

Department of Chemistry, Chemistry Research Laboratory, University of Oxford, UK.

Macromolecule Content

Total Structure Weight: 92.81 kDa
Atom Count: 6,238
Modelled Residue Count: 710
Deposited Residue Count: 792
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific demethylase 4A	A, B	381	Homo sapiens	Mutation(s): 0 Gene Names: KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677 EC: 1.14.11
UniProt & NIH Common Fund Data Resources
Find proteins for O75164 (Homo sapiens) Explore O75164 Go to UniProtKB: O75164
PHAROS: O75164 GTEx: ENSG00000066135
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O75164
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H1.4	C, D	15	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P10412 (Homo sapiens) Explore P10412 Go to UniProtKB: P10412
PHAROS: P10412 GTEx: ENSG00000168298
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10412
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OGA Query on OGA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain O [auth B] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B]	H [auth A], O [auth B]	N-OXALYLGLYCINE C₄ H₅ N O₅ BIMZLRFONYSTPT-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain O [auth B] Interactions & Density Focus chain H [auth A] Focus chain O [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain P [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain P [auth B]	I [auth A], J [auth A], K [auth A], P [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B]	F [auth A], M [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain M [auth B]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain E [auth A]	E [auth A], L [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain L [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth B] MOL2 format, chain G [auth A] MOL2 format, chain N [auth B]	G [auth A], N [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain N [auth B] Interactions & Density Focus chain G [auth A] Focus chain N [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
M3L Query on M3L	C, D	L-PEPTIDE LINKING	C₉ H₂₁ N₂ O₂		LYS

Binding Affinity Annotations
ID	Source	Binding Affinity
OGA	BindingDB: 6H8P	IC50: min: 8.50e+4, max: 2.50e+5 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.212
R-Value Work: 0.192
R-Value Observed: 0.193
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.722	α = 90
b = 150.146	β = 90
c = 57.601	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2018-08-15

Deposition Author(s):

Chowdhury, R.

Walport, L.J.

Schofield, C.J.

Revision History (Full details and data files)

Version 1.0: 2018-08-15
Type: Initial release
Version 1.1: 2018-09-12
Changes: Data collection, Database references
Version 1.2: 2018-10-24
Changes: Data collection, Database references
Version 1.3: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description