› 6a57

X-ray diffraction
2.7Å resolution

Structure of histone demethylase REF6 complexed with DNA

Released:
DOI: 10.2210/pdb6a57/pdb
PDB entry 6a57 coloured by chain, front view.
PDB entry 6a57 coloured by chain, side view.
PDB entry 6a57 coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Crystal structures of REF6 and its complex with DNA reveal diverse recognition mechanisms.
Tian Z, Li X, Li M, Wu W, Zhang M, Tang C, Li Z, Liu Y, Chen Z, Yang M, Ma L, Caba C, Tong Y, Lam HM, Dai S, Chen Z
Cell Discov 6 17 (2020)
PMID: 32257379

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119546 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Lysine-specific demethylase REF6 Chain: A
Molecule details ›
Chain: A
Length: 140 amino acids
Theoretical weight: 16.52 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9STM3 (Residues: 1223-1360; Coverage: 10%)
Gene names: At3g48430, EIN6, JMJ12, PKDM9A, REF6, T29H11_50
DNA (5'-D(*CP*TP*TP*TP*CP*TP*CP*TP*GP*TP*TP*TP*TP*GP*TP*C)-3') Chain: B
Molecule details ›
Chain: B
Length: 16 nucleotides
Theoretical weight: 4.81 KDa
Source organism: Arabidopsis thaliana
Expression system: Not provided
DNA (5'-D(*GP*GP*AP*CP*AP*AP*AP*AP*CP*AP*GP*AP*GP*AP*AP*A)-3') Chain: C
Molecule details ›
Chain: C
Length: 16 nucleotides
Theoretical weight: 4.98 KDa
Source organism: Arabidopsis thaliana
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ZN 4 x ZN
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P3221
Unit cell:
a: 96.087Å b: 96.087Å c: 73.905Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.223 0.221 0.257
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

4 review citations

Dynamics of H3K27me3 Modification on Plant Adaptation to Environmental Cues.
Shen et al. (2021)
3 more

1 mention without citation

AlphaFill: enriching AlphaFold models with ligands and cofactors.
Hekkelman et al. (2023)