Summary information

PDB id
7q6l
Class
RNA
Method
NMR
Summary
Solution structure of an intramolecular RNA g-quadruplex formed by the 6a8a17u mutant from a 22mer guanine-rich sequence within the 5'utr of bcl-2 proto-oncogene
Reference
Wang Z, Jurt S, Dominguez-Martin A, Johannsen S, Sigel RKO: "Solution structure of an intramolecular RNA G-quadruplex formed by the 6A8A17U mutant from a 22mer guanine-rich sequence within the 5'UTR of BCL-2 proto-oncogene."
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=3333 groove=---- planarity=0.335 type=other  nts=4 GGGG A.G1,A.G9,A.G13,A.G20
 2 glyco-bond=---- sugar=3333 groove=---- planarity=0.218 type=other  nts=4 GGGG A.G2,A.G10,A.G14,A.G21
 3 glyco-bond=---- sugar=3-33 groove=---- planarity=0.393 type=other  nts=4 GGGG A.G3,A.G11,A.G15,A.G22

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=3333 groove=---- WC-->Major nts=4 GGGG A.G1,A.G9,A.G13,A.G20
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G2,A.G10,A.G14,A.G21
 3  glyco-bond=---- sugar=3-33 groove=---- WC-->Major nts=4 GGGG A.G3,A.G11,A.G15,A.G22
  step#1  pm(>>,forward)  area=11.90 rise=3.35 twist=31.9
  step#2  pm(>>,forward)  area=11.01 rise=3.86 twist=26.1
  strand#1 RNA glyco-bond=--- sugar=333 nts=3 GGG A.G1,A.G2,A.G3
  strand#2 RNA glyco-bond=--- sugar=33- nts=3 GGG A.G9,A.G10,A.G11
  strand#3 RNA glyco-bond=--- sugar=333 nts=3 GGG A.G13,A.G14,A.G15
  strand#4 RNA glyco-bond=--- sugar=333 nts=3 GGG A.G20,A.G21,A.G22

Download PDB file
Interactive view in 3Dmol.js
2 stacking diagrams 
 1  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G1,A.G9,A.G13,A.G20
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G2,A.G10,A.G14,A.G21
  step#1  pm(>>,forward)  area=11.90 rise=3.35 twist=31.9

Download PDB file
Interactive view in 3Dmol.js

 
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G2,A.G10,A.G14,A.G21
 3  glyco-bond=---- sugar=3-33 groove=---- WC-->Major nts=4 GGGG A.G3,A.G11,A.G15,A.G22
  step#2  pm(>>,forward)  area=11.01 rise=3.86 twist=26.1

Download PDB file
Interactive view in 3Dmol.js

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=3333 groove=---- WC-->Major nts=4 GGGG A.G1,A.G9,A.G13,A.G20
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G2,A.G10,A.G14,A.G21
 3  glyco-bond=---- sugar=3-33 groove=---- WC-->Major nts=4 GGGG A.G3,A.G11,A.G15,A.G22
  step#1  pm(>>,forward)  area=11.90 rise=3.35 twist=31.9
  step#2  pm(>>,forward)  area=11.01 rise=3.86 twist=26.1
  strand#1  U RNA glyco-bond=--- sugar=333 nts=3 GGG A.G1,A.G2,A.G3
  strand#2  U RNA glyco-bond=--- sugar=33- nts=3 GGG A.G9,A.G10,A.G11
  strand#3  U RNA glyco-bond=--- sugar=333 nts=3 GGG A.G13,A.G14,A.G15
  strand#4  U RNA glyco-bond=--- sugar=333 nts=3 GGG A.G20,A.G21,A.G22
  loop#1 type=propeller strands=[#1,#2] nts=5 CCAUA A.C4,A.C5,A.A6,A.U7,A.A8
  loop#2 type=propeller strands=[#2,#3] nts=1 U A.U12
  loop#3 type=propeller strands=[#3,#4] nts=4 AUCU A.A16,A.U17,A.C18,A.U19

Download PDB file
Interactive view in 3Dmol.js