› 6a5n

X-ray diffraction
2.4Å resolution

Crystal structure of Arabidopsis thaliana SUVH6 in complex with methylated DNA

Released:
DOI: 10.2210/pdb6a5n/pdb
PDB entry 6a5n coloured by chain, front view.
PDB entry 6a5n coloured by chain, side view.
PDB entry 6a5n coloured by chain, top view.
Source organisms:
Primary publication:
Mechanistic insights into plant SUVH family H3K9 methyltransferases and their binding to context-biased non-CG DNA methylation.
Li X, Harris CJ, Zhong Z, Chen W, Liu R, Jia B, Wang Z, Li S, Jacobsen SE, Du J
Proc Natl Acad Sci U S A 115 E8793-E8802 (2018)
PMID: 30150382

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + a [histone H3]-L-lysine(9) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(9)
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119547 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH6 Chain: A
Molecule details ›
Chain: A
Length: 527 amino acids
Theoretical weight: 59.06 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8VZ17 (Residues: 264-790; Coverage: 67%)
Gene names: At2g22740, SDG23, SET23, SUVH6, T9I22.18
Sequence domains:
Structure domains: SET domain
DNA (5'-D(*GP*AP*GP*TP*AP*CP*TP*(5CM)P*AP*GP*CP*AP*GP*T)-3') Chain: C
Molecule details ›
Chain: C
Length: 14 nucleotides
Theoretical weight: 4.32 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*CP*AP*CP*TP*GP*CP*TP*GP*AP*GP*TP*AP*CP*T)-3') Chain: D
Molecule details ›
Chain: D
Length: 14 nucleotides
Theoretical weight: 4.26 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 3 x ZN
1 modified residue:
Ligand 5CM 1 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P212121
Unit cell:
a: 74.137Å b: 79.443Å c: 107.845Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.233 0.23 0.279
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

11 review citations

Establishment, maintenance, and biological roles of non-CG methylation in plants.
Kenchanmane Raju et al. (2019)
10 more

2 mentions without citation

Mechanistic insights into plant SUVH family H3K9 methyltransferases and their binding to context-biased non-CG DNA methylation.
Li et al. (2018)
1 more