› 6jnm

X-ray diffraction
2.05Å resolution

REF6 ZnF2-4-NAC004-mC3 complex

Released:
DOI: 10.2210/pdb6jnm/pdb
PDB entry 6jnm coloured by chain, front view.
PDB entry 6jnm coloured by chain, side view.
PDB entry 6jnm coloured by chain, top view.
Source organisms:
Primary publication:
DNA methylation repels targeting of Arabidopsis REF6.
Qiu Q, Mei H, Deng X, He K, Wu B, Yao Q, Zhang J, Lu F, Ma J, Cao X
Nat Commun 10 2063 (2019)
PMID: 31048693

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-120085 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Lysine-specific demethylase REF6 Chains: A, B
Molecule details ›
Chains: A, B
Length: 101 amino acids
Theoretical weight: 12.03 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9STM3 (Residues: 1260-1360; Coverage: 7%)
Gene names: At3g48430, EIN6, JMJ12, PKDM9A, REF6, T29H11_50
DNA (5'-D(*TP*TP*CP*TP*(5CM)P*TP*GP*TP*TP*TP*TP*G)-3') Chains: D, F
Molecule details ›
Chains: D, F
Length: 12 nucleotides
Theoretical weight: 3.64 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*CP*AP*AP*AP*AP*CP*AP*GP*AP*GP*AP*A)-3') Chains: C, E
Molecule details ›
Chains: C, E
Length: 12 nucleotides
Theoretical weight: 3.7 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 6 x ZN
1 modified residue:
Ligand 5CM 2 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P43
Unit cell:
a: 88.516Å b: 88.516Å c: 72.33Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.201 0.2 0.228
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

6 review citations

Epigenetic Regulation of Auxin Homeostasis.
Mateo-Bonmatí et al. (2019)
5 more

1 mention without citation

Crystal structures of REF6 and its complex with DNA reveal diverse recognition mechanisms.
Tian et al. (2020)