Summary information

PDB id
7zj4
Class
RNA
Method
cryo-EM (4.43 Å)
Summary
Ligand bound state of a brocolli-pepper aptamer fret tile
Reference
McRae EKS, Vallina NS, Hansen BK, Boussebayle A, Andersen ES: "Structure determination of Pepper-Broccoli FRET pair by RNA origami scaffolding."
Abstract
 
G4 notes
2 G-tetrads, 1 G4 helix, 1 G4 stem, 2(-PD+P), (2+2), UUDD

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 2 G-tetrads

 1 glyco-bond=--s- sugar=-333 groove=-wn- planarity=0.297 type=other  nts=4 GGGG E.G172,E.G176,E.G202,E.G198
 2 glyco-bond=--ss sugar=-3-3 groove=-w-n planarity=0.230 type=other  nts=4 GGGG E.G173,E.G177,E.G200,E.G195

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, 2 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=--s- sugar=-333 groove=-wn- WC-->Major nts=4 GGGG E.G172,E.G176,E.G202,E.G198
 2  glyco-bond=--ss sugar=-3-3 groove=-w-n WC-->Major nts=4 GGGG E.G173,E.G177,E.G200,E.G195
  step#1  pm(>>,forward)  area=11.53 rise=3.27 twist=27.5
  strand#1 RNA glyco-bond=-- sugar=-- nts=2 GG E.G172,E.G173
  strand#2 RNA glyco-bond=-- sugar=33 nts=2 GG E.G176,E.G177
  strand#3 RNA glyco-bond=ss sugar=3- nts=2 GG E.G202,E.G200
  strand#4 RNA glyco-bond=-s sugar=33 nts=2 GG E.G198,E.G195

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1 stacking diagram 
 1  glyco-bond=--s- sugar=-333 groove=-wn- WC-->Major nts=4 GGGG E.G172,E.G176,E.G202,E.G198
 2  glyco-bond=--ss sugar=-3-3 groove=-w-n WC-->Major nts=4 GGGG E.G173,E.G177,E.G200,E.G195
  step#1  pm(>>,forward)  area=11.53 rise=3.27 twist=27.5

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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, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUDD, anti-parallel, 2(-PD+P), (2+2)

 1  glyco-bond=--s- sugar=-333 groove=-wn- WC-->Major nts=4 GGGG E.G172,E.G176,E.G202,E.G198
 2  glyco-bond=--ss sugar=-3-3 groove=-w-n WC-->Major nts=4 GGGG E.G173,E.G177,E.G200,E.G195
  step#1  pm(>>,forward)  area=11.53 rise=3.27 twist=27.5
  strand#1  U RNA glyco-bond=-- sugar=-- nts=2 GG E.G172,E.G173
  strand#2  U RNA glyco-bond=-- sugar=33 nts=2 GG E.G176,E.G177
  strand#3* D RNA glyco-bond=ss sugar=3- nts=2 GG E.G202,E.G200 bulged-nts=1 U E.U201
  strand#4* D RNA glyco-bond=-s sugar=33 nts=2 GG E.G198,E.G195 bulged-nts=2 AU E.A197,E.U196
  loop#1 type=propeller strands=[#1,#2] nts=2 UC E.U174,E.C175
  loop#2 type=diagonal  strands=[#2,#4] nts=17 GUCCAGUUCGCUGUCGA E.G178,E.U179,E.C180,E.C181,E.A182,E.G183,E.U184,E.U185,E.C186,E.G187,E.C188,E.U189,E.G190,E.U191,E.C192,E.G193,E.A194
  loop#3 type=propeller strands=[#4,#3] nts=1 A E.A199

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