› 3q0d

X-ray diffraction
2.37Å resolution

Crystal structure of SUVH5 SRA- hemi methylated CG DNA complex

Released:
DOI: 10.2210/pdb3q0d/pdb
PDB entry 3q0d coloured by chain, front view.
PDB entry 3q0d coloured by chain, side view.
PDB entry 3q0d coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
A dual flip-out mechanism for 5mC recognition by the Arabidopsis SUVH5 SRA domain and its impact on DNA methylation and H3K9 dimethylation in vivo.
Rajakumara E, Law JA, Simanshu DK, Voigt P, Johnson LM, Reinberg D, Patel DJ, Jacobsen SE
Genes Dev 25 137-52 (2011)
PMID: 21245167

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-116732 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH5 Chains: A, X
Molecule details ›
Chains: A, X
Length: 167 amino acids
Theoretical weight: 18.52 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli BL21(DE3)
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
DNA (5'-D(*TP*CP*CP*AP*(5CM)P*GP*TP*CP*AP*G)-3') Chain: B
Molecule details ›
Chain: B
Length: 10 nucleotides
Theoretical weight: 3.02 KDa
Source organism: Arabidopsis thaliana
Expression system: Not provided
DNA (5'-D(*CP*TP*GP*AP*CP*GP*TP*GP*GP*A)-3') Chain: C
Molecule details ›
Chain: C
Length: 10 nucleotides
Theoretical weight: 3.09 KDa
Source organism: Arabidopsis thaliana
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand CL 1 x CL
1 modified residue:
Ligand 5CM 1 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P42
Unit cell:
a: 76.379Å b: 76.379Å c: 74.254Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.226 0.225 0.263
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

10 review citations

Histone methylation: a dynamic mark in health, disease and inheritance.
Greer et al. (2012)
9 more

3 mentions without citation

A Structural Perspective on Readout of Epigenetic Histone and DNA Methylation Marks.
Patel DJ. (2016)
2 more