› 5vc9

X-ray diffraction
2.1Å resolution

Zinc finger of human CXXC4 in complex with CpG DNA

Released:
DOI: 10.2210/pdb5vc9/pdb
PDB entry 5vc9 coloured by chain, front view.
PDB entry 5vc9 coloured by chain, side view.
PDB entry 5vc9 coloured by chain, top view.
Source organisms:
Primary publication:
DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants.
Xu C, Liu K, Lei M, Yang A, Li Y, Hughes TR, Min J
Structure 26 85-95.e3 (2018)
PMID: 29276034

Function and Biology Details

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-119275 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
CXXC-type zinc finger protein 4 Chains: C, F
Molecule details ›
Chains: C, F
Length: 49 amino acids
Theoretical weight: 5.61 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9H2H0 (Residues: 133-180; Coverage: 24%)
Gene names: CXXC4, IDAX
Sequence domains: CXXC zinc finger domain
CpG DNA Chains: A, B, D, E
Molecule details ›
Chains: A, B, D, E
Length: 12 nucleotides
Theoretical weight: 3.66 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand UNX 7 x UNX
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P1
Unit cell:
a: 29.983Å b: 40.29Å c: 57.76Å
α: 70.98° β: 86.43° γ: 67.83°
R-values:
R R work R free
0.213 0.211 0.248
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

9 review citations

Understanding the interplay between CpG island-associated gene promoters and H3K4 methylation.
Hughes et al. (2020)
8 more

1 mention without citation

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