› 4ft2

X-ray diffraction
3.2Å resolution

crystal structure of Zea mays ZMET2 in complex H3(1-15)K9me2 peptide and SAH

Released:
DOI: 10.2210/pdb4ft2/pdb
PDB entry 4ft2 coloured by chain, front view.
PDB entry 4ft2 coloured by chain, side view.
PDB entry 4ft2 coloured by chain, top view.
Source organisms:
Primary publication:
Dual binding of chromomethylase domains to H3K9me2-containing nucleosomes directs DNA methylation in plants.
Du J, Zhong X, Bernatavichute YV, Stroud H, Feng S, Caro E, Vashisht AA, Terragni J, Chin HG, Tu A, Hetzel J, Wohlschlegel JA, Pradhan S, Patel DJ, Jacobsen SE
Cell 151 167-80 (2012)
PMID: 23021223

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + DNA = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosine
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159439 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
DNA (cytosine-5)-methyltransferase 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 784 amino acids
Theoretical weight: 87.59 KDa
Source organism: Zea mays
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9AXT8 (Residues: 130-912; Coverage: 86%)
Gene name: MET2A
Sequence domains:
Structure domains:
Histone H3.1 Chain: P
Molecule details ›
Chain: P
Length: 15 amino acids
Theoretical weight: 1.59 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 2-16; Coverage: 11%)
Gene names: H3C1, H3C10, H3C11, H3C12, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3FA, H3FB, H3FC HIST1H3C, H3FD, H3FF, H3FH, H3FI, H3FJ, H3FK, H3FL, HIST1H3A, HIST1H3B, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J

Ligands and Environments


Cofactor: Ligand SAH 2 x SAH
No bound ligands
1 modified residue:
Ligand MLY 1 x MLY

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P1
Unit cell:
a: 64.861Å b: 88.858Å c: 113.501Å
α: 93.15° β: 95.72° γ: 110.7°
R-values:
R R work R free
0.237 0.235 0.277
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

61 review citations

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

10 mentions without citation

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