› 6asd

X-ray diffraction
1.85Å resolution

Zinc finger region of human TET1 in complex with CpG DNA

Released:
DOI: 10.2210/pdb6asd/pdb
PDB entry 6asd coloured by chain, front view.
PDB entry 6asd coloured by chain, side view.
PDB entry 6asd 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-119582 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Methylcytosine dioxygenase TET1 Chain: C
Molecule details ›
Chain: C
Length: 47 amino acids
Theoretical weight: 5.5 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8NFU7 (Residues: 587-632; Coverage: 2%)
Gene names: CXXC6, KIAA1676, LCX, TET1
Sequence domains: CXXC zinc finger domain
DNA (5'-D(*GP*CP*CP*AP*CP*CP*GP*GP*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 17 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: C2
Unit cell:
a: 73.502Å b: 31.951Å c: 65.414Å
α: 90° β: 121.82° γ: 90°
R-values:
R R work R free
0.203 0.202 0.235
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

3 mentions without citation

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