› 4qen

X-ray diffraction
2Å resolution

crystal structure of KRYPTONITE in complex with mCHH DNA and SAH

Released:
DOI: 10.2210/pdb4qen/pdb
PDB entry 4qen coloured by chain, front view.
PDB entry 4qen coloured by chain, side view.
PDB entry 4qen coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Mechanism of DNA methylation-directed histone methylation by KRYPTONITE.
Du J, Johnson LM, Groth M, Feng S, Hale CJ, Li S, Vashisht AA, Wohlschlegel JA, Patel DJ, Jacobsen SE, Jacobsen SE
Mol Cell 55 495-504 (2014)
PMID: 25018018

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-118013 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 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
DNA (5'-D(*GP*GP*TP*AP*CP*TP*(5CM)P*AP*TP*CP*AP*GP*TP*AP*T)-3') Chain: C
Molecule details ›
Chain: C
Length: 15 nucleotides
Theoretical weight: 4.6 KDa
Source organism: Arabidopsis thaliana
Expression system: Not provided
DNA (5'-D(*AP*CP*TP*GP*AP*TP*GP*AP*GP*TP*AP*CP*CP*AP*T)-3') Chain: D
Molecule details ›
Chain: D
Length: 15 nucleotides
Theoretical weight: 4.59 KDa
Source organism: Arabidopsis thaliana
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand SAH 1 x SAH
Ligand ZN 4 x ZN
1 modified residue:
Ligand 5CM 1 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P212121
Unit cell:
a: 54.395Å b: 98.009Å c: 122.581Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.178 0.176 0.211
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

28 review citations

Dynamics and function of DNA methylation in plants.
Zhang et al. (2018)
27 more

4 mentions without citation

DNA methylation pathways and their crosstalk with histone methylation.
Du et al. (2015)
3 more