6L8M image
Entry Detail
PDB ID:
6L8M
Keywords:
DNA
Title:
WNT DNA promoter mutant G-quadruplex
Biological Source:
Source Organism:
Homo sapiens
PDB Version:
Deposition Date:
2019-11-06
Release Date:
2019-12-11
Method Details:
Experimental Method:
SOLUTION NMR
Conformers Calculated:
100
Conformers Submitted:
10
Selection Criteria:
structures with the lowest energy
6L8M validation report
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(*GP*GP*GP*TP*CP*AP*CP*CP*GP*GP*GP*CP*AP*GP*TP*GP*GP*GP*CP*GP*GP*G)-3')
Chain IDs:A
Chain Length:22
Number of Molecules:1
Biological Source:Homo sapiens
Ligand Molecules
NA
Primary Citation
Cytosine epigenetic modification modulates the formation of an unprecedented G4 structure in the WNT1 promoter.
Nucleic Acids Res. 48 1120 1130 (2020)
PMID: 31912153 DOI: 10.1093/nar/gkz1207

Abstact

Time-resolved imino proton nuclear magnetic resonance spectra of the WT22m sequence d(GGGCCACCGGGCAGTGGGCGGG), derived from the WNT1 promoter region, revealed an intermediate G-quadruplex G4(I) structure during K+-induced conformational transition from an initial hairpin structure to the final G4(II) structure. Moreover, a single-base C-to-T mutation at either position C4 or C7 of WT22m could lock the intermediate G4(I) structure without further conformational change to the final G4(II) structure. Surprisingly, we found that the intermediate G4(I) structure is an atypical G4 structure, which differs from a typical hybrid G4 structure of the final G4(II) structure. Further studies of modified cytosine analogues associated with epigenetic regulation indicated that slight modification on a cytosine could modulate G4 structure. A simplified four-state transition model was introduced to describe such conformational transition and disclose the possible mechanism for G4 structural selection caused by cytosine modification.

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Primary Citation of related structures
6L8M