DSSR-curated G4 structure: PDB entry 2rsk

Summary information

PDB id: 2rsk
Class: membrane protein-RNA
Method: NMR
Summary: RNA aptamer against prion protein in complex with the partial binding peptide
Reference: Mashima T, Nishikawa F, Kamatari YO, Fujiwara H, Saimura M, Nagata T, Kodaki T, Nishikawa S, Kuwata K, Katahira M (2013): "Anti-prion activity of an RNA aptamer and its structural basis." Nucleic Acids Res., 41, 1355-1362. doi: 10.1093/nar/gks1132.
Abstract: Prion proteins (PrPs) cause prion diseases, such as bovine spongiform encephalopathy. The conversion of a normal cellular form (PrP(C)) of PrP into an abnormal form (PrP(Sc)) is thought to be associated with the pathogenesis. An RNA aptamer that tightly binds to and stabilizes PrP(C) is expected to block this conversion and to thereby prevent prion diseases. Here, we show that an RNA aptamer comprising only 12 residues, r(GGAGGAGGAGGA) (R12), reduces the PrP(Sc) level in mouse neuronal cells persistently infected with the transmissible spongiform encephalopathy agent. Nuclear magnetic resonance analysis revealed that R12, folded into a unique quadruplex structure, forms a dimer and that each monomer simultaneously binds to two portions of the N-terminal half of PrP(C), resulting in tight binding. Electrostatic and stacking interactions contribute to the affinity of each portion. Our results demonstrate the therapeutic potential of an RNA aptamer as to prion diseases.
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=0.264 type=other  nts=4 GGGG A.G1,A.G4,A.G7,A.G10
 2 glyco-bond=---- sugar=---. groove=---- planarity=0.371 type=bowl   nts=4 GGGG A.G2,A.G5,A.G8,A.G11
 3 glyco-bond=---- sugar=-3-3 groove=---- planarity=0.269 type=other  nts=4 GGGG B.G13,B.G16,B.G19,B.G22
 4 glyco-bond=---- sugar=---. groove=---- planarity=0.365 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=3-3- 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=12.60 rise=2.75 twist=33.6 step#2 mm(<>,outward) area=19.42 rise=2.97 twist=0.4 step#3 pm(>>,forward) area=12.61 rise=2.75 twist=33.7 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=--3. 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=12.60 rise=2.75 twist=33.6 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=3-3- groove=---- Major-->WC nts=4 GGGG B.G16,B.G13,B.G22,B.G19 step#2 mm(<>,outward) area=19.42 rise=2.97 twist=0.4 Download PDB file Interactive view in 3Dmol.js
	3 glyco-bond=---- sugar=3-3- 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=12.61 rise=2.75 twist=33.7 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=12.60 rise=2.75 twist=33.6
  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=-3-3 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=12.61 rise=2.75 twist=33.7
  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=3. 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