› 8tci

X-ray diffraction
3.19Å resolution

Crystal structure of DNMT3C-DNMT3L in complex with CGG DNA

Released:
DOI: 10.2210/pdb8tci/pdb
PDB entry 8tci coloured by chain, front view.
PDB entry 8tci coloured by chain, side view.
PDB entry 8tci coloured by chain, top view.
Source organisms:
Primary publication:
The structure of DNA methyltransferase DNMT3C reveals an activity-tuning mechanism for DNA methylation.
Khudaverdyan N, Lu J, Chen X, Herle G, Song J
J Biol Chem 107633 (2024)
PMID: 39098534

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-270788 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (3 distinct):
DNA (cytosine-5)-methyltransferase 3C Chains: A, D
Molecule details ›
Chains: A, D
Length: 284 amino acids
Theoretical weight: 32.54 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0DOY1 (Residues: 458-740; Coverage: 38%)
Gene names: Dnmt3c, Gm14490
Sequence domains: C-5 cytosine-specific DNA methylase
DNA (cytosine-5)-methyltransferase 3-like Chains: B, C
Molecule details ›
Chains: B, C
Length: 199 amino acids
Theoretical weight: 23.02 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9UJW3 (Residues: 181-379; Coverage: 52%)
Gene name: DNMT3L
(5'-D(P*CP*AP*TP*G)-R(P*(PYO))-D(P*GP*GP*TP*CP*TP*AP*AP*TP*TP*AP*GP*AP*CP*CP*GP*CP*AP*TP*G)-3') Chains: E, F
Molecule details ›
Chains: E, F
Length: 24 nucleotides
Theoretical weight: 7.37 KDa

Ligands and Environments


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

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.2
Spacegroup: P21
Unit cell:
a: 63.088Å b: 189.509Å c: 62.864Å
α: 90° β: 90.07° γ: 90°
R-values:
R R work R free
0.228 0.225 0.257
Expression system: Escherichia coli BL21(DE3)

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