DSSR-curated G4 structure: PDB entry 2ru7

Summary information

PDB id: 2ru7
Class: membrane protein-RNA
Method: NMR
Summary: Refined structure of RNA aptamer in complex with the partial binding peptide of prion protein
Reference: Hayashi T, Oshima H, Mashima T, Nagata T, Katahira M, Kinoshita M (2014): "Binding of an RNA aptamer and a partial peptide of a prion protein: crucial importance of water entropy in molecular recognition." Nucleic Acids Res., 42, 6861-6875. doi: 10.1093/nar/gku382.
Abstract
G4 notes: 4 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack, 2(-P-P-P), parallel(4+0), UUUU, coaxial interfaces: 5'/5'

Base-block schematics in six views

PyMOL session file	PDB file	View in 3Dmol.js

List of 4 G-tetrads

 1 glyco-bond=---- sugar=-3-3 groove=---- planarity=0.218 type=other  nts=4 GGGG A.G1,A.G4,A.G7,A.G10
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.312 type=bowl   nts=4 GGGG A.G2,A.G5,A.G8,A.G11
 3 glyco-bond=---- sugar=-3-- groove=---- planarity=0.225 type=other  nts=4 GGGG B.G13,B.G16,B.G19,B.G22
 4 glyco-bond=---- sugar=---- groove=---- planarity=0.341 type=bowl   nts=4 GGGG B.G14,B.G17,B.G20,B.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, 4 G-tetrad layers, inter-molecular, with 2 stems

	1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.G2,A.G5,A.G8,A.G11 2* glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GGGG A.G1,A.G4,A.G7,A.G10 3 glyco-bond=---- sugar=3--- groove=---- Major-->WC nts=4 GGGG B.G16,B.G13,B.G22,B.G19 4 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG B.G17,B.G14,B.G23,B.G20 step#1 mp(<<,backward) area=12.01 rise=3.32 twist=31.3 step#2 mm(<>,outward) area=22.82 rise=3.46 twist=6.7 step#3 pm(>>,forward) area=11.28 rise=3.40 twist=29.2 strand#1 RNA glyco-bond=---- sugar=--3- nts=4 GGGG A.G2,A.G1,B.G16,B.G17 strand#2 RNA glyco-bond=---- sugar=-3-- nts=4 GGGG A.G5,A.G4,B.G13,B.G14 strand#3 RNA glyco-bond=---- sugar=---- nts=4 GGGG A.G8,A.G7,B.G22,B.G23 strand#4 RNA glyco-bond=---- sugar=-3-- nts=4 GGGG A.G11,A.G10,B.G19,B.G20 Download PDB file Interactive view in 3Dmol.js
3 stacking diagrams
	1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.G2,A.G5,A.G8,A.G11 2* glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GGGG A.G1,A.G4,A.G7,A.G10 step#1 mp(<<,backward) area=12.01 rise=3.32 twist=31.3 Download PDB file Interactive view in 3Dmol.js
	2* glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GGGG A.G1,A.G4,A.G7,A.G10 3 glyco-bond=---- sugar=3--- groove=---- Major-->WC nts=4 GGGG B.G16,B.G13,B.G22,B.G19 step#2 mm(<>,outward) area=22.82 rise=3.46 twist=6.7 Download PDB file Interactive view in 3Dmol.js
	3 glyco-bond=---- sugar=3--- groove=---- Major-->WC nts=4 GGGG B.G16,B.G13,B.G22,B.G19 4 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG B.G17,B.G14,B.G23,B.G20 step#3 pm(>>,forward) area=11.28 rise=3.40 twist=29.2 Download PDB file Interactive view in 3Dmol.js

List of 2 G4-stems

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)

 1  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GGGG A.G1,A.G4,A.G7,A.G10
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.G2,A.G5,A.G8,A.G11
  step#1  pm(>>,forward)  area=12.01 rise=3.32 twist=31.3
  strand#1  U RNA glyco-bond=-- sugar=-- nts=2 GG A.G1,A.G2
  strand#2  U RNA glyco-bond=-- sugar=3- nts=2 GG A.G4,A.G5
  strand#3  U RNA glyco-bond=-- sugar=-- nts=2 GG A.G7,A.G8
  strand#4  U RNA glyco-bond=-- sugar=3- nts=2 GG A.G10,A.G11
  loop#1 type=propeller strands=[#1,#2] nts=1 A A.A3
  loop#2 type=propeller strands=[#2,#3] nts=1 A A.A6
  loop#3 type=propeller strands=[#3,#4] nts=1 A A.A9

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Interactive view in 3Dmol.js

Stem#2, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)

 1  glyco-bond=---- sugar=-3-- groove=---- WC-->Major nts=4 GGGG B.G13,B.G16,B.G19,B.G22
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.G14,B.G17,B.G20,B.G23
  step#1  pm(>>,forward)  area=11.28 rise=3.40 twist=29.2
  strand#1  U RNA glyco-bond=-- sugar=-- nts=2 GG B.G13,B.G14
  strand#2  U RNA glyco-bond=-- sugar=3- nts=2 GG B.G16,B.G17
  strand#3  U RNA glyco-bond=-- sugar=-- nts=2 GG B.G19,B.G20
  strand#4  U RNA glyco-bond=-- sugar=-- nts=2 GG B.G22,B.G23
  loop#1 type=propeller strands=[#1,#2] nts=1 A B.A15
  loop#2 type=propeller strands=[#2,#3] nts=1 A B.A18
  loop#3 type=propeller strands=[#3,#4] nts=1 A B.A21