Summary information and primary citation

PDB-id
7zj5
Class
RNA
Method
cryo-EM (4.55 Å)
Summary
Unbound 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, UUDD, anti-parallel:basket2, 2+2, 2(-PD+P)

Cartoon-block schematics in six views (download the tarball)

PyMOL session file

Download PDB file

View in 3Dmol.js

List of 2 G-tetrads

 1 glyco-bond=--s- sugar=-333 groove=-wn- planarity=0.389 type=bowl-2 N+ nts=4 GGGG 1:E.G172,1:E.G176,1:E.G202,1:E.G198
 2 glyco-bond=--ss sugar=-3-3 groove=-w-n planarity=0.367 type=other  N+ nts=4 GGGG 1:E.G173,1:E.G177,1:E.G200,1: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-tetrads, INTRA-molecular, with 1 stem
 1  glyco-bond=--s- sugar=-333 groove=-wn- WC-->Major N+ nts=4 GGGG 1:E.G172,1:E.G176,1:E.G202,1:E.G198
 2  glyco-bond=--ss sugar=-3-3 groove=-w-n WC-->Major N+ nts=4 GGGG 1:E.G173,1:E.G177,1:E.G200,1:E.G195
  step#1  pm(>>,forward)  area=9.40  rise=3.31 twist=35.3
  strand#1 RNA glyco-bond=-- sugar=-- nts=2 GG 1:E.G172,1:E.G173
  strand#2 RNA glyco-bond=-- sugar=33 nts=2 GG 1:E.G176,1:E.G177
  strand#3 RNA glyco-bond=ss sugar=3- nts=2 GG 1:E.G202,1:E.G200
  strand#4 RNA glyco-bond=-s sugar=33 nts=2 GG 1:E.G198,1:E.G195

Download PDB file
Interactive view in 3Dmol.js
1 stacking diagram 
 1  glyco-bond=--s- sugar=-333 groove=-wn- WC-->Major N+ nts=4 GGGG 1:E.G172,1:E.G176,1:E.G202,1:E.G198
 2  glyco-bond=--ss sugar=-3-3 groove=-w-n WC-->Major N+ nts=4 GGGG 1:E.G173,1:E.G177,1:E.G200,1:E.G195
  step#1  pm(>>,forward)  area=9.40  rise=3.31 twist=35.3

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, 2 G-tetrads, 3 loops, INTRA-molecular, UUDD, anti-parallel:basket2, 2+2, 2(-PD+P)
 1  glyco-bond=--s- sugar=-333 groove=-wn- WC-->Major N+ nts=4 GGGG 1:E.G172,1:E.G176,1:E.G202,1:E.G198
 2  glyco-bond=--ss sugar=-3-3 groove=-w-n WC-->Major N+ nts=4 GGGG 1:E.G173,1:E.G177,1:E.G200,1:E.G195
  step#1  pm(>>,forward)  area=9.40  rise=3.31 twist=35.3
  strand#1  U RNA glyco-bond=-- sugar=-- nts=2 GG 1:E.G172,1:E.G173
  strand#2  U RNA glyco-bond=-- sugar=33 nts=2 GG 1:E.G176,1:E.G177
  strand#3* D RNA glyco-bond=ss sugar=3- nts=2 GG 1:E.G202,1:E.G200 bulged-nts=1 U 1:E.U201
  strand#4* D RNA glyco-bond=-s sugar=33 nts=2 GG 1:E.G198,1:E.G195 bulged-nts=2 AU 1:E.A197,1:E.U196
  loop#1 type=propeller strands=[#1,#2] nts=2 UC 1:E.U174,1:E.C175
  loop#2 type=diagonal  strands=[#2,#4] nts=17 GUCCAGUUCGCUGUCGA 1:E.G178,1:E.U179,1:E.C180,1:E.C181,1:E.A182,1:E.G183,1:E.U184,1:E.U185,1:E.C186,1:E.G187,1:E.C188,1:E.U189,1:E.G190,1:E.U191,1:E.C192,1:E.G193,1:E.A194
  loop#3 type=propeller strands=[#4,#3] nts=1 A 1:E.A199

Download PDB file
Interactive view in 3Dmol.js