› 4z3c

X-ray diffraction
1.57Å resolution

Zinc finger region of human TET3 in complex with CpG DNA

Released:
DOI: 10.2210/pdb4z3c/pdb
PDB entry 4z3c coloured by chain, front view.
PDB entry 4z3c coloured by chain, side view.
PDB entry 4z3c 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-118350 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Methylcytosine dioxygenase TET3 Chain: C
Molecule details ›
Chain: C
Length: 52 amino acids
Theoretical weight: 5.9 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O43151 (Residues: 47-98; Coverage: 3%)
Gene names: KIAA0401, TET3
Sequence domains: CXXC zinc finger domain
DNA (5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3') 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

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

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P21
Unit cell:
a: 27.616Å b: 54.744Å c: 40.228Å
α: 90° β: 103.53° γ: 90°
R-values:
R R work R free
0.216 0.215 0.252
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