› 6ip0

X-ray diffraction
2.4Å resolution

Crystal structure of Arabidopsis thaliana JMJ13 catalytic domain in complex with AKG

Released:
DOI: 10.2210/pdb6ip0/pdb
PDB entry 6ip0 coloured by chain, front view.
PDB entry 6ip0 coloured by chain, side view.
PDB entry 6ip0 coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
The Arabidopsis H3K27me3 demethylase JUMONJI 13 is a temperature and photoperiod dependent flowering repressor.
Zheng S, Hu H, Ren H, Yang Z, Qiu Q, Qi W, Liu X, Chen X, Cui X, Li S, Zhou B, Sun D, Cao X, Du J
OpenAccess logo Nat Commun 10 1303 (2019)
PMID: 30899015

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-123491 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lysine-specific demethylase JMJ13 Chain: A
Molecule details ›
Chain: A
Length: 490 amino acids
Theoretical weight: 55.34 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: F4KIX0 (Residues: 90-578; Coverage: 62%)
Gene names: At5g46910, JMJ13, MQD22.4
Sequence domains:

Ligands and Environments

4 bound ligands:
Ligand AKG 1 x AKG
Ligand NI 1 x NI
Ligand ZN 2 x ZN
Ligand SO4 13 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P6222
Unit cell:
a: 129.67Å b: 129.67Å c: 231.52Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.193 0.192 0.212
Expression system: Escherichia coli BL21(DE3)

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Citations

12 review citations

Role of Chromatin Architecture in Plant Stress Responses: An Update.
Bhadouriya et al. (2020)
11 more