› 4c5x

X-ray diffraction
1.3Å resolution

Ultra High Resolution Dickerson-Drew dodecamer B-DNA with 5-Hydroxymethyl-cytosine Modification

Released:
DOI: 10.2210/pdb4c5x/pdb
PDB entry 4c5x coloured by chain, front view.
PDB entry 4c5x coloured by chain, side view.
PDB entry 4c5x coloured by chain, top view.
Source organism: synthetic construct
Primary publication:
Structural insights into how 5-hydroxymethylation influences transcription factor binding.
Lercher L, McDonough MA, El-Sagheer AH, Thalhammer A, Kriaucionis S, Brown T, Schofield CJ
Chem Commun (Camb) 50 1794-6 (2014)
PMID: 24287551

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117277 (preferred)
Entry contents:
1 distinct DNA molecule
Macromolecule:
5'-D(CP*GP*CP*GP*AP*AP*TP*TP*5HCP*GP*CP*GP)-3' Chains: A, B
Molecule details ›
Chains: A, B
Length: 12 nucleotides
Theoretical weight: 3.69 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MG 1 x MG
1 modified residue:
Ligand 5HC 2 x 5HC

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P212121
Unit cell:
a: 25.3Å b: 40.27Å c: 64.88Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.145 0.142 0.173
Expression system: Not provided

Quick links

Citations

8 review citations

TET proteins in natural and induced differentiation.
Scott-Browne et al. (2017)
7 more

2 mentions without citation

Making the bend: DNA tertiary structure and protein-DNA interactions.
Harteis et al. (2014)
1 more