› 5w9s

X-ray diffraction
2.1Å resolution

Zinc finger of human CXXC5 in complex with CpG DNA

Released:
DOI: 10.2210/pdb5w9s/pdb
PDB entry 5w9s coloured by chain, front view.
PDB entry 5w9s coloured by chain, side view.
PDB entry 5w9s 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-119340 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
CXXC-type zinc finger protein 5 Chain: C
Molecule details ›
Chain: C
Length: 71 amino acids
Theoretical weight: 8.34 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q7LFL8 (Residues: 254-306; Coverage: 17%)
Gene names: CXXC5, HSPC195, TCCCIA00297
Sequence domains: CXXC zinc finger domain
CpG DNA fragment Chains: A, B
Molecule details ›
Chains: A, B
Length: 12 nucleotides
Theoretical weight: 3.66 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand ZN 2 x ZN
Ligand SO4 1 x SO4
Ligand UNX 1 x UNX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E SUPERBRIGHT
Spacegroup: P32
Unit cell:
a: 40.11Å b: 40.11Å c: 81.2Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.22 0.218 0.254
Expression systems:
  • Escherichia coli
  • 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)