› 5yko

X-ray diffraction
2.9Å resolution

Crystal structure of Arabidopsis thaliana JMJ14 catalytic domain in complex with NOG and H3K4me3 peptide

Released:
DOI: 10.2210/pdb5yko/pdb
PDB entry 5yko coloured by chain, front view.
PDB entry 5yko coloured by chain, side view.
PDB entry 5yko coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Structure of the Arabidopsis JMJ14-H3K4me3 Complex Provides Insight into the Substrate Specificity of KDM5 Subfamily Histone Demethylases.
Yang Z, Qiu Q, Chen W, Jia B, Chen X, Hu H, He K, Deng X, Li S, Tao WA, Cao X, Du J
Plant Cell 30 167-177 (2018)
PMID: 29233856

Function and Biology Details

Reaction catalysed: 
(1a) a [histone H3]-N(6),N(6),N(6)-trimethyl-L-lysine(4) + 2-oxoglutarate + O(2) = a [histone H3]-N(6),N(6)-dimethyl-L-lysine(4) + succinate + formaldehyde + CO(2)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-157784 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Lysine-specific demethylase JMJ14 Chain: A
Molecule details ›
Chain: A
Length: 564 amino acids
Theoretical weight: 65 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8GUI6 (Residues: 35-597; Coverage: 59%)
Gene names: At4g20400, F9F13.50, JMJ14, JMJ4, PKDM7B
Sequence domains:
Histone H3.1 Chain: P
Molecule details ›
Chain: P
Length: 10 amino acids
Theoretical weight: 1.19 KDa
Source organism: Arabidopsis thaliana
Expression system: Not provided
UniProt:
  • Canonical: P59226 (Residues: 2-11; Coverage: 7%)
Gene names: At1g09200, At3g27360, At5g10390, At5g10400, At5g65360, F12B17_250, F12B17_260, HTR1, HTR13, HTR2, HTR3, HTR9, K1G2.8, MNA5.9, T12M4.9

Ligands and Environments

3 bound ligands:
Ligand NI 1 x NI
Ligand ZN 2 x ZN
Ligand OGA 1 x OGA
1 modified residue:
Ligand M3L 1 x M3L

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P212121
Unit cell:
a: 68.639Å b: 100.113Å c: 109.405Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.206 0.204 0.244
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Repair of DNA double-strand breaks in plant meiosis: role of eukaryotic RecA recombinases and their modulators.
Emmenecker et al. (2023)
1 more

2 mentions without citation

The Arabidopsis H3K27me3 demethylase JUMONJI 13 is a temperature and photoperiod dependent flowering repressor.
Zheng et al. (2019)
1 more