› 4ygi

X-ray diffraction
2.6Å resolution

Crystal Structure of SUVH5 SRA bound to fully hydroxymethylated CG DNA

Released:
DOI: 10.2210/pdb4ygi/pdb
PDB entry 4ygi coloured by chain, front view.
PDB entry 4ygi coloured by chain, side view.
PDB entry 4ygi coloured by chain, top view.
Source organisms:
Primary publication:
Mechanistic insights into the recognition of 5-methylcytosine oxidation derivatives by the SUVH5 SRA domain.
Rajakumara E, Nakarakanti NK, Nivya MA, Satish M
Sci Rep 6 20161 (2016)
PMID: 26841909

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118318 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH5 Chain: A
Molecule details ›
Chain: A
Length: 167 amino acids
Theoretical weight: 18.52 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: O82175 (Residues: 362-528; Coverage: 21%)
Gene names: At2g35160, SDG9, SET9, SUVH5, T4C15.17
Sequence domains: SAD/SRA domain
Structure domains: SRA-YDG
Polydeoxyribonucleotide Chain: B
Molecule details ›
Chain: B
Length: 11 nucleotides
Theoretical weight: 3.38 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MG 3 x MG
1 modified residue:
Ligand 5HC 1 x 5HC

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P42212
Unit cell:
a: 76.98Å b: 76.98Å c: 72.111Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.237 0.234 0.283
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

7 citation in other articles

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

2 mentions without citation

Detecting and interpreting DNA methylation marks.
Ren et al. (2018)
1 more