4qeo

X-ray diffraction
2Å resolution

crystal structure of KRYPTONITE in complex with mCHH DNA, H3(1-15) peptide and SAH

Released:

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:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-118014 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4 Chain: A
Molecule details ›
Chain: A
Length: 533 amino acids
Theoretical weight: 59.69 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8GZB6 (Residues: 93-624; Coverage: 85%)
Gene names: At5g13960, KYP, MAC12.7, SDG33, SET33, SUVH4
Sequence domains:
Structure domains: SET domain
Histone H3.2 Chain: P
Molecule details ›
Chain: P
Length: 15 amino acids
Theoretical weight: 1.57 KDa
Source organism: Xenopus laevis
Expression system: Not provided
UniProt:
  • Canonical: P84233 (Residues: 2-16; Coverage: 11%)
DNA 5'-GGTACT(5CM)ATCAGTAT-3' Chain: C
Molecule details ›
Chain: C
Length: 15 nucleotides
Theoretical weight: 4.6 KDa
DNA 5'-ACTGATGAGTACCAT-3' Chain: D
Molecule details ›
Chain: D
Length: 15 nucleotides
Theoretical weight: 4.59 KDa

Ligands and Environments

2 bound ligands:
1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P212121
Unit cell:
a: 55.46Å b: 96.765Å c: 122.411Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.188 0.186 0.226
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided