› 4m9v

X-ray diffraction
0.97Å resolution

Zfp57 mutant (E182Q) in complex with 5-carboxylcytosine DNA

Released:
DOI: 10.2210/pdb4m9v/pdb
PDB entry 4m9v coloured by chain, front view.
PDB entry 4m9v coloured by chain, side view.
PDB entry 4m9v coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
DNA recognition of 5-carboxylcytosine by a Zfp57 mutant at an atomic resolution of 0.97 Å.
Liu Y, Olanrewaju YO, Zhang X, Cheng X
Biochemistry 52 9310-7 (2013)
PMID: 24236546

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero trimer (preferred)
hetero hexamer
Assembly name:
PDBe Complex ID:
PDB-CPX-117841 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Zinc finger protein 57 Chains: C, F
Molecule details ›
Chains: C, F
Length: 64 amino acids
Theoretical weight: 7.38 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') Chains: A, D
Molecule details ›
Chains: A, D
Length: 11 nucleotides
Theoretical weight: 3.36 KDa
Source organism: Mus musculus
Expression system: Not provided
DNA (5'-D(*AP*CP*TP*GP*(1CC)P*GP*GP*CP*AP*AP*T)-3') Chains: B, E
Molecule details ›
Chains: B, E
Length: 11 nucleotides
Theoretical weight: 3.4 KDa
Source organism: Mus musculus
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P21
Unit cell:
a: 36.388Å b: 96.093Å c: 36.408Å
α: 90° β: 113.14° γ: 90°
R-values:
R R work R free
0.131 0.13 0.143
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Recognition of Oxidized 5-Methylcytosine Derivatives in DNA by Natural and Engineered Protein Scaffolds.
Muñoz-López et al. (2018)
12 other articles

5 mentions without citation

Detecting and interpreting DNA methylation marks.
Ren et al. (2018)
4 more