Summary information

PDB id
8vjt
Class
RNA
Method
X-ray (1.052 Å)
Summary
Structure of the poly-ug quadruplex (gugugu)4
Reference
Roschdi S, Montemayor EJ, Vivek R, Bingman CA, Butcher SE (2024): "Self-assembly and condensation of intermolecular poly(UG) RNA quadruplexes." Nucleic Acids Res. doi: 10.1093/nar/gkae870.
Abstract
Poly(UG) or 'pUG' dinucleotide repeats are highly abundant sequences in eukaryotic RNAs. In Caenorhabditis elegans, pUGs are added to RNA 3' ends to direct gene silencing within Mutator foci, a germ granule condensate. Here, we show that pUG RNAs efficiently self-assemble into gel condensates through quadruplex (G4) interactions. Short pUG sequences form right-handed intermolecular G4s (pUG G4s), while longer pUGs form left-handed intramolecular G4s (pUG folds). We determined a 1.05 Å crystal structure of an intermolecular pUG G4, which reveals an eight stranded G4 dimer involving 48 nucleotides, 7 different G and U quartet conformations, 7 coordinated potassium ions, 8 sodium ions and a buried water molecule. A comparison of the intermolecular pUG G4 and intramolecular pUG fold structures provides insights into the molecular basis for G4 handedness and illustrates how a simple dinucleotide repeat sequence can form complex structures with diverse topologies.
G4 notes
3 G-tetrads, 1 G4 helix

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 3 G-tetrads

 1 glyco-bond=ssss sugar=---- groove=---- planarity=0.073 type=planar nts=4 GGGG 1:A.G1,3:A.G1,2:A.G1,4:A.G1
 2 glyco-bond=---- sugar=3333 groove=---- planarity=0.230 type=other  nts=4 GGGG 1:A.G3,4:A.G3,2:A.G3,3:A.G3
 3 glyco-bond=---- sugar=3333 groove=---- planarity=0.379 type=bowl   nts=4 GGGG 1:A.G5,4:A.G5,2:A.G5,3:A.G5

List of 1 G4-helix

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, inter-molecular

 1  glyco-bond=ssss sugar=---- groove=---- Major-->WC nts=4 GGGG 1:A.G1,3:A.G1,2:A.G1,4:A.G1
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:A.G3,4:A.G3,2:A.G3,3:A.G3
 3  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:A.G5,4:A.G5,2:A.G5,3:A.G5
  step#1  pm(>>,forward)  area=6.13  rise=3.06 twist=143.2
  step#2  pm(>>,forward)  area=0.00  rise=7.39 twist=61.0
  strand#1 RNA glyco-bond=s-- sugar=-33 nts=3 GGG 1:A.G1,1:A.G3,1:A.G5
  strand#2 RNA glyco-bond=s-- sugar=-33 nts=3 GGG 3:A.G1,4:A.G3,4:A.G5
  strand#3 RNA glyco-bond=s-- sugar=-33 nts=3 GGG 2:A.G1,2:A.G3,2:A.G5
  strand#4 RNA glyco-bond=s-- sugar=-33 nts=3 GGG 4:A.G1,3:A.G3,3:A.G5

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2 stacking diagrams 
 1  glyco-bond=ssss sugar=---- groove=---- Major-->WC nts=4 GGGG 1:A.G1,3:A.G1,2:A.G1,4:A.G1
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:A.G3,4:A.G3,2:A.G3,3:A.G3
  step#1  pm(>>,forward)  area=6.13  rise=3.06 twist=143.2

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 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:A.G3,4:A.G3,2:A.G3,3:A.G3
 3  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:A.G5,4:A.G5,2:A.G5,3:A.G5
  step#2  pm(>>,forward)  area=0.00  rise=7.39 twist=61.0

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