4C5X image
Deposition Date 2013-09-16
Release Date 2013-10-02
Last Version Date 2023-12-20
Entry Detail
PDB ID:
4C5X
Keywords:
DNA
Title:
Ultra High Resolution Dickerson-Drew dodecamer B-DNA with 5-Hydroxymethyl-cytosine Modification
Biological Source:
Source Organism:
SYNTHETIC CONSTRUCT (Taxon ID: 32630)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
1.30 Å
R-Value Free:
0.17
R-Value Work:
0.14
R-Value Observed:
0.14
Space Group:
P 21 21 21
4C5X validation report
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Molecule:5'-D(CP*GP*CP*GP*AP*AP*TP*TP*5HCP*GP*CP*GP)-3'
Chain IDs:A, B
Chain Length:12
Number of Molecules:2
Biological Source:SYNTHETIC CONSTRUCT
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
5HC A DC ?
Ligand Molecules
MG
Primary Citation
Structural insights into how 5-hydroxymethylation influences transcription factor binding.
Chem. Commun. (Camb.) 50 1794 1796 (2014)
PMID: 24287551 DOI: 10.1039/c3cc48151d

Abstact

Transcription factor binding and high resolution crystallographic studies (1.3 Å) of Dickerson-Drew duplexes with cytosine, methylcytosine and hydroxymethylcytosine bases provide evidence that C-5 cytosine modifications could regulate transcription by context dependent effects on DNA transcription factor interactions.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
4C63
4C64