DSSR-curated G4 structure: PDB entry 2rqj

Summary information

PDB id: 2rqj
Class: RNA
Method: NMR
Summary: Quadruplex structure of an RNA aptamer against bovine prion protein
Reference: Mashima T, Matsugami A, Nishikawa F, Nishikawa S, Katahira M (2009): "Unique quadruplex structure and interaction of an RNA aptamer against bovine prion protein." Nucleic Acids Res., 37, 6249-6258. doi: 10.1093/nar/gkp647.
Abstract: RNA aptamers against bovine prion protein (bPrP) were obtained, most of the obtained aptamers being found to contain the r(GGAGGAGGAGGA) (R12) sequence. Then, it was revealed that R12 binds to both bPrP and its beta-isoform with high affinity. Here, we present the structure of R12. This is the first report on the structure of an RNA aptamer against prion protein. R12 forms an intramolecular parallel quadruplex. The quadruplex contains G:G:G:G tetrad and G(:A):G:G(:A):G hexad planes. Two quadruplexes form a dimer through intermolecular hexad-hexad stacking. Two lysine clusters of bPrP have been identified as binding sites for R12. The electrostatic interaction between the uniquely arranged phosphate groups of R12 and the lysine clusters is suggested to be responsible for the affinity of R12 to bPrP. The stacking interaction between the G:G:G:G tetrad planes and tryptophan residues may also contribute to the affinity. One R12 dimer molecule is supposed to simultaneously bind the two lysine clusters of one bPrP molecule, resulting in even higher affinity. The atomic coordinates of R12 would be useful for the development of R12 as a therapeutic agent against prion diseases and Alzheimer's disease.
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=0.092 type=planar nts=4 GGGG A.G1,A.G4,A.G7,A.G10
 2 glyco-bond=---- sugar=---3 groove=---- planarity=0.076 type=planar nts=4 GGGG A.G2,A.G5,A.G8,A.G11
 3 glyco-bond=---- sugar=-3-3 groove=---- planarity=0.112 type=planar nts=4 GGGG B.G13,B.G16,B.G19,B.G22
 4 glyco-bond=---- sugar=---3 groove=---- planarity=0.075 type=planar 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=---3 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=--3- groove=---- Major-->WC nts=4 GGGG B.G17,B.G14,B.G23,B.G20 step#1 mp(<<,backward) area=11.25 rise=3.18 twist=35.2 step#2 mm(<>,outward) area=19.27 rise=3.39 twist=5.3 step#3 pm(>>,forward) area=11.51 rise=3.17 twist=35.6 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=--33 nts=4 GGGG A.G8,A.G7,B.G22,B.G23 strand#4 RNA glyco-bond=---- sugar=33-- 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=---3 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=11.25 rise=3.18 twist=35.2 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=19.27 rise=3.39 twist=5.3 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=--3- groove=---- Major-->WC nts=4 GGGG B.G17,B.G14,B.G23,B.G20 step#3 pm(>>,forward) area=11.51 rise=3.17 twist=35.6 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=---3 groove=---- WC-->Major nts=4 GGGG A.G2,A.G5,A.G8,A.G11
  step#1  pm(>>,forward)  area=11.25 rise=3.18 twist=35.2
  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=33 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=---3 groove=---- WC-->Major nts=4 GGGG B.G14,B.G17,B.G20,B.G23
  step#1  pm(>>,forward)  area=11.51 rise=3.17 twist=35.6
  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=33 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