› 4gzn

X-ray diffraction
0.99Å resolution

Mouse ZFP57 zinc fingers in complex with methylated DNA

Released:
DOI: 10.2210/pdb4gzn/pdb
PDB entry 4gzn coloured by chain, front view.
PDB entry 4gzn coloured by chain, side view.
PDB entry 4gzn coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
An atomic model of Zfp57 recognition of CpG methylation within a specific DNA sequence.
Liu Y, Toh H, Sasaki H, Zhang X, Cheng X
Genes Dev 26 2374-9 (2012)
PMID: 23059534

Function and Biology Details

Biochemical function:
  • not assigned
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-117570 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Zinc finger protein 57 Chain: C
Molecule details ›
Chain: C
Length: 60 amino acids
Theoretical weight: 7.05 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8C6P8 (Residues: 137-195; Coverage: 14%)
Gene name: Zfp57
Sequence domains: Zinc finger, C2H2 type
Structure domains: Classic Zinc Finger
DNA (5'-D(*TP*AP*TP*TP*GP*CP*(5CM)P*GP*CP*AP*G)-3') Chain: A
Molecule details ›
Chain: A
Length: 11 nucleotides
Theoretical weight: 3.36 KDa
Source organism: Mus musculus
Expression system: Not provided
DNA (5'-D(*AP*CP*TP*GP*(5CM)P*GP*GP*CP*AP*AP*T)-3') Chain: B
Molecule details ›
Chain: B
Length: 11 nucleotides
Theoretical weight: 3.37 KDa
Source organism: Mus musculus
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand CA 1 x CA
Ligand MPD 2 x MPD
Ligand ZN 2 x ZN
Ligand ACT 1 x ACT
1 modified residue:
Ligand 5CM 2 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: C2221
Unit cell:
a: 40.218Å b: 60.641Å c: 96.119Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.132 0.131 0.14
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

19 review citations

DNA methylation dynamics during epigenetic reprogramming in the germline and preimplantation embryos.
Messerschmidt et al. (2014)
18 more

13 mentions without citation

On how mammalian transcription factors recognize methylated DNA.
Buck-Koehntop et al. (2013)
12 more