Summary information and primary citation

PDB-id
8k85
Class
RNA
Method
X-ray (2.95 Å)
Summary
Crystal structure of red broccoli aptamer with obi
Reference
Peng X, Huang L: "Structural analysis of various Broccoli aptamers with different Fluorophores."
Abstract
 
G4 notes
4 G-tetrads, 2 G4 helices, 2 G4 stems, UUDD, anti-parallel:basket2, 2+2

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

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List of 4 G-tetrads

 1 glyco-bond=--s- sugar=-33. groove=-wn- planarity=0.290 type=other  -- nts=4 GGGG 1:A.G7,1:A.G11,1:B.G48,1:B.G44
 2 glyco-bond=--ss sugar=-3-3 groove=-w-n planarity=0.155 type=planar -- nts=4 GGGG 1:A.G8,1:A.G12,1:B.G46,1:B.G41
 3 glyco-bond=ss-- sugar=3-3- groove=-w-n planarity=0.176 type=other  -- nts=4 GGGG 1:A.G41,1:A.G46,1:B.G12,1:B.G8
 4 glyco-bond=---s sugar=.-33 groove=--wn planarity=0.330 type=other  -- nts=4 GGGG 1:A.G44,1:B.G7,1:B.G11,1:A.G48

List of 2 G4-helices

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, inter-molecular, with 1 stem
 1  glyco-bond=--s- sugar=-33. groove=-wn- WC-->Major -- nts=4 GGGG 1:A.G7,1:A.G11,1:B.G48,1:B.G44
 2  glyco-bond=--ss sugar=-3-3 groove=-w-n WC-->Major -- nts=4 GGGG 1:A.G8,1:A.G12,1:B.G46,1:B.G41
  step#1  pm(>>,forward)  area=8.67  rise=3.29 twist=34.1
  strand#1 RNA glyco-bond=-- sugar=-- nts=2 GG 1:A.G7,1:A.G8
  strand#2 RNA glyco-bond=-- sugar=33 nts=2 GG 1:A.G11,1:A.G12
  strand#3 RNA glyco-bond=ss sugar=3- nts=2 GG 1:B.G48,1:B.G46
  strand#4 RNA glyco-bond=-s sugar=.3 nts=2 GG 1:B.G44,1:B.G41

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1 stacking diagram 
 1  glyco-bond=--s- sugar=-33. groove=-wn- WC-->Major -- nts=4 GGGG 1:A.G7,1:A.G11,1:B.G48,1:B.G44
 2  glyco-bond=--ss sugar=-3-3 groove=-w-n WC-->Major -- nts=4 GGGG 1:A.G8,1:A.G12,1:B.G46,1:B.G41
  step#1  pm(>>,forward)  area=8.67  rise=3.29 twist=34.1

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Helix#2, 2 G-tetrads, inter-molecular, with 1 stem
 1  glyco-bond=ss-- sugar=3-3- groove=-w-n Major-->WC -- nts=4 GGGG 1:A.G41,1:A.G46,1:B.G12,1:B.G8
 2  glyco-bond=-s-- sugar=.33- groove=nw-- Major-->WC -- nts=4 GGGG 1:A.G44,1:A.G48,1:B.G11,1:B.G7
  step#1  mp(<<,backward) area=9.89  rise=3.33 twist=33.5
  strand#1 RNA glyco-bond=s- sugar=3. nts=2 GG 1:A.G41,1:A.G44
  strand#2 RNA glyco-bond=ss sugar=-3 nts=2 GG 1:A.G46,1:A.G48
  strand#3 RNA glyco-bond=-- sugar=33 nts=2 GG 1:B.G12,1:B.G11
  strand#4 RNA glyco-bond=-- sugar=-- nts=2 GG 1:B.G8,1:B.G7

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1 stacking diagram 
 1  glyco-bond=ss-- sugar=3-3- groove=-w-n Major-->WC -- nts=4 GGGG 1:A.G41,1:A.G46,1:B.G12,1:B.G8
 2  glyco-bond=-s-- sugar=.33- groove=nw-- Major-->WC -- nts=4 GGGG 1:A.G44,1:A.G48,1:B.G11,1:B.G7
  step#1  mp(<<,backward) area=9.89  rise=3.33 twist=33.5

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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-tetrads, 2 loops, inter-molecular, UUDD, anti-parallel:basket2, 2+2
 1  glyco-bond=--s- sugar=-33. groove=-wn- WC-->Major -- nts=4 GGGG 1:A.G7,1:A.G11,1:B.G48,1:B.G44
 2  glyco-bond=--ss sugar=-3-3 groove=-w-n WC-->Major -- nts=4 GGGG 1:A.G8,1:A.G12,1:B.G46,1:B.G41
  step#1  pm(>>,forward)  area=8.67  rise=3.29 twist=34.1
  strand#1  U RNA glyco-bond=-- sugar=-- nts=2 GG 1:A.G7,1:A.G8
  strand#2  U RNA glyco-bond=-- sugar=33 nts=2 GG 1:A.G11,1:A.G12
  strand#3* D RNA glyco-bond=ss sugar=3- nts=2 GG 1:B.G48,1:B.G46 bulged-nts=1 U 1:B.U47
  strand#4* D RNA glyco-bond=-s sugar=.3 nts=2 GG 1:B.G44,1:B.G41 bulged-nts=2 AU 1:B.A43,1:B.U42
  loop#1 type=propeller strands=[#1,#2] nts=2 UC 1:A.U9,1:A.C10
  loop#2 type=propeller strands=[#4,#3] nts=1 U 1:B.U45

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Stem#2, 2 G-tetrads, 2 loops, inter-molecular, UUDD, anti-parallel:basket2, 2+2
 1  glyco-bond=ss-- sugar=3-3- groove=-w-n Major-->WC -- nts=4 GGGG 1:A.G41,1:A.G46,1:B.G12,1:B.G8
 2  glyco-bond=-s-- sugar=.33- groove=nw-- Major-->WC -- nts=4 GGGG 1:A.G44,1:A.G48,1:B.G11,1:B.G7
  step#1  mp(<<,backward) area=9.89  rise=3.33 twist=33.5
  strand#1* U RNA glyco-bond=s- sugar=3. nts=2 GG 1:A.G41,1:A.G44 bulged-nts=2 UA 1:A.U42,1:A.A43
  strand#2* U RNA glyco-bond=ss sugar=-3 nts=2 GG 1:A.G46,1:A.G48 bulged-nts=1 U 1:A.U47
  strand#3  D RNA glyco-bond=-- sugar=33 nts=2 GG 1:B.G12,1:B.G11
  strand#4  D RNA glyco-bond=-- sugar=-- nts=2 GG 1:B.G8,1:B.G7
  loop#1 type=propeller strands=[#1,#2] nts=1 U 1:A.U45
  loop#2 type=propeller strands=[#4,#3] nts=2 UC 1:B.U9,1:B.C10

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