DSSR-derived G-quadruplex features in PDB entry 2la5
- RNA binding protein-RNA
- RNA duplex-quadruplex junction complex with fmrp rgg peptide
- Phan, A.T., Kuryavyi, V., Darnell, J.C., Serganov, A., Majumdar, A., Ilin, S., Raslin, T., Polonskaia, A., Chen, C., Clain, D., Darnell, R.B., Patel, D.J.: (2011) "Structure-function studies of FMRP RGG peptide recognition of an RNA duplex-quadruplex junction." Nat.Struct.Mol.Biol., 18, 796-804.
- We have determined the solution structure of the complex between an arginine-glycine-rich RGG peptide from the human fragile X mental retardation protein (FMRP) and an in vitro-selected guanine-rich (G-rich) sc1 RNA. The bound RNA forms a newly discovered G-quadruplex separated from the flanking duplex stem by a mixed junctional tetrad. The RGG peptide is positioned along the major groove of the RNA duplex, with the G-quadruplex forcing a sharp turn of R(10)GGGGR(15) at the duplex-quadruplex junction. Arg10 and Arg15 form cross-strand specificity-determining intermolecular hydrogen bonds with the major-groove edges of guanines of adjacent Watson-Crick G•C pairs. Filter-binding assays on RNA and peptide mutations identify and validate contributions of peptide-RNA intermolecular contacts and shape complementarity to molecular recognition. These findings on FMRP RGG domain recognition by a combination of G-quadruplex and surrounding RNA sequences have implications for the recognition of other genomic G-rich RNAs.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem · 2(-P-P-P), parallel(4+0), UUUU · negative twist
1 glyco-bond=---- groove=---- planarity=0.176 type=other nts=4 GGGG A.G6,A.G9,A.G26,A.G18 2 glyco-bond=---- groove=---- planarity=0.195 type=other nts=4 GGGG A.G11,A.G15,A.G20,A.G24 3 glyco-bond=---- groove=---- planarity=0.106 type=planar nts=4 GGGG A.G12,A.G16,A.G21,A.G25
In DSSR, a G4-helix is defined by stacking interactions of G-tetrads, regardless of backbone connectivity, and may contain more than one G4-stem.
Helix#1, 3 G-tetrad layers, INTRA-molecular, with 1 stem
In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands.
Stem#1, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)
List of 1 non-stem G4-loop (including the two closing Gs)
1 type=lateral helix=#1 nts=4 GGUG A.G6,A.G7,A.U8,A.G9