Summary information

PDB id
7ps8
Class
virus
Method
NMR
Summary
NMR structure of the u3 RNA g-quadruplex
Reference
Marquevielle J, Amrane S: "NMR Structure of the U3 RNA G-quadruplex."
Abstract
 
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, 3(-P-P-P), parallel(4+0), UUUU

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 3 G-tetrads

 1 glyco-bond=---- sugar=3-.3 groove=---- planarity=0.320 type=other  nts=4 GGGG A.G3,A.G7,A.G17,A.G21
 2 glyco-bond=---- sugar=3-33 groove=---- planarity=0.286 type=other  nts=4 GGGG A.G4,A.G8,A.G18,A.G22
 3 glyco-bond=-s-- sugar=-3.3 groove=wn-- planarity=0.358 type=other  nts=4 GGGG A.G5,A.G12,A.G19,A.G23

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, INTRA-molecular, with 1 stem

 1  glyco-bond=---- sugar=3-.3 groove=---- WC-->Major nts=4 GGGG A.G3,A.G7,A.G17,A.G21
 2  glyco-bond=---- sugar=3-33 groove=---- WC-->Major nts=4 GGGG A.G4,A.G8,A.G18,A.G22
 3  glyco-bond=-s-- sugar=-3.3 groove=wn-- WC-->Major nts=4 GGGG A.G5,A.G12,A.G19,A.G23
  step#1  pm(>>,forward)  area=15.52 rise=3.46 twist=23.3
  step#2  pm(>>,forward)  area=15.71 rise=3.38 twist=29.7
  strand#1 RNA glyco-bond=--- sugar=33- nts=3 GGG A.G3,A.G4,A.G5
  strand#2 RNA glyco-bond=--s sugar=--3 nts=3 GGG A.G7,A.G8,A.G12
  strand#3 RNA glyco-bond=--- sugar=.3. nts=3 GGG A.G17,A.G18,A.G19
  strand#4 RNA glyco-bond=--- sugar=333 nts=3 GGG A.G21,A.G22,A.G23

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2 stacking diagrams 
 1  glyco-bond=---- sugar=3-.3 groove=---- WC-->Major nts=4 GGGG A.G3,A.G7,A.G17,A.G21
 2  glyco-bond=---- sugar=3-33 groove=---- WC-->Major nts=4 GGGG A.G4,A.G8,A.G18,A.G22
  step#1  pm(>>,forward)  area=15.52 rise=3.46 twist=23.3

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 2  glyco-bond=---- sugar=3-33 groove=---- WC-->Major nts=4 GGGG A.G4,A.G8,A.G18,A.G22
 3  glyco-bond=-s-- sugar=-3.3 groove=wn-- WC-->Major nts=4 GGGG A.G5,A.G12,A.G19,A.G23
  step#2  pm(>>,forward)  area=15.71 rise=3.38 twist=29.7

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List of 1 G4-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, 3 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 3(-P-P-P), parallel(4+0)

 1  glyco-bond=---- sugar=3-.3 groove=---- WC-->Major nts=4 GGGG A.G3,A.G7,A.G17,A.G21
 2  glyco-bond=---- sugar=3-33 groove=---- WC-->Major nts=4 GGGG A.G4,A.G8,A.G18,A.G22
 3  glyco-bond=-s-- sugar=-3.3 groove=wn-- WC-->Major nts=4 GGGG A.G5,A.G12,A.G19,A.G23
  step#1  pm(>>,forward)  area=15.52 rise=3.46 twist=23.3
  step#2  pm(>>,forward)  area=15.71 rise=3.38 twist=29.7
  strand#1  U RNA glyco-bond=--- sugar=33- nts=3 GGG A.G3,A.G4,A.G5
  strand#2* U RNA glyco-bond=--s sugar=--3 nts=3 GGG A.G7,A.G8,A.G12 bulged-nts=3 UGU A.U9,A.G10,A.U11
  strand#3  U RNA glyco-bond=--- sugar=.3. nts=3 GGG A.G17,A.G18,A.G19
  strand#4  U RNA glyco-bond=--- sugar=333 nts=3 GGG A.G21,A.G22,A.G23
  loop#1 type=propeller strands=[#1,#2] nts=1 A A.A6
  loop#2 type=propeller strands=[#2,#3] nts=4 GCCU A.G13,A.C14,A.C15,A.U16
  loop#3 type=propeller strands=[#3,#4] nts=1 C A.C20

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