3R1D: Crystal structure of GC(8BrG)GCGGCGGC duplex

Citation:
Abstract
The CGG repeats are present in the 5'-untranslated region (5'-UTR) of the fragile X mental retardation gene FMR1 and are associated with two diseases: fragile X-associated tremor ataxia syndrome (FXTAS) and fragile X syndrome (FXS). FXTAS occurs when the number of repeats is 55-200 and FXS develops when the number exceeds 200. FXTAS is an RNA-mediated disease in which the expanded CGG tracts form stable structures and sequester important RNA binding proteins. We obtained and analysed three crystal structures of double-helical CGG repeats involving unmodified and 8-Br modified guanosine residues. Despite the presence of the non-canonical base pairs, the helices retain an A-form. In the G-G pairs one guanosine is always in the syn conformation, the other is anti. There are two hydrogen bonds between the Watson-Crick edge of G(anti) and the Hoogsteen edge of G(syn): O6.N1H and N7.N2H. The G(syn)-G(anti) pair shows affinity for binding ions in the major groove. G(syn) causes local unwinding of the helix, compensated elsewhere along the duplex. CGG helical structures appear relatively stable compared with CAG and CUG tracts. This could be an important factor in the RNA's ligand binding affinity and specificity.
PDB ID: 3R1DDownload
MMDB ID: 91020
PDB Deposition Date: 2011/3/10
Updated in MMDB: 2017/11
Experimental Method:
x-ray diffraction
Resolution: 1.45  Å
Biological Unit for 3R1D: dimeric; determined by author and by software (PISA)
Molecular Components in 3R1D
Label Count Molecule
Nucleotide(1 molecule)
2
RNA (5'-r(*gp*cp*(grb)p*gp*cp*gp*gp*cp*gp*gp*c)-3')
Molecule annotation
Chemicals (5 molecules)
1
2
2
3
* Click molecule labels to explore molecular sequence information.

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