Summary information and primary citation

PDB-id
9nap
Class
RNA
Method
cryo-EM (3.01 Å)
Summary
RNA scaffold attached to mango in the presence of to1-biotin
Reference
Jones CP, Ferre-D'Amare AR: "Symmetric scaffolds enable de novo modelling of RNA by cryoEM."
Abstract
 
G4 notes
2 G-tetrads, 1 G4 helix, 1 G4 stem, UUUD, hybrid2, 3+1, 2(-P-P-Lw)

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

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List of 2 G-tetrads

 1 glyco-bond=---s sugar=-33- groove=--wn planarity=0.406 type=other  O+ nts=4 GGGG A.G40,A.G44,A.G49,A.G56
 2 glyco-bond=---s sugar=-3-3 groove=--wn planarity=0.402 type=other  O+ nts=4 GGGG A.G41,A.G45,A.G50,A.G54

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=-33- groove=--wn WC-->Major O+ nts=4 GGGG A.G40,A.G44,A.G49,A.G56
 2  glyco-bond=---s sugar=-3-3 groove=--wn WC-->Major O+ nts=4 GGGG A.G41,A.G45,A.G50,A.G54
  step#1  pm(>>,forward)  area=9.93  rise=3.51 twist=29.1
  strand#1 RNA glyco-bond=-- sugar=-- nts=2 GG A.G40,A.G41
  strand#2 RNA glyco-bond=-- sugar=33 nts=2 GG A.G44,A.G45
  strand#3 RNA glyco-bond=-- sugar=3- nts=2 GG A.G49,A.G50
  strand#4 RNA glyco-bond=ss sugar=-3 nts=2 GG A.G56,A.G54

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1 stacking diagram 
 1  glyco-bond=---s sugar=-33- groove=--wn WC-->Major O+ nts=4 GGGG A.G40,A.G44,A.G49,A.G56
 2  glyco-bond=---s sugar=-3-3 groove=--wn WC-->Major O+ nts=4 GGGG A.G41,A.G45,A.G50,A.G54
  step#1  pm(>>,forward)  area=9.93  rise=3.51 twist=29.1

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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-tetrads, 3 loops, INTRA-molecular, UUUD, hybrid2, 3+1, 2(-P-P-Lw)
 1  glyco-bond=---s sugar=-33- groove=--wn WC-->Major O+ nts=4 GGGG A.G40,A.G44,A.G49,A.G56
 2  glyco-bond=---s sugar=-3-3 groove=--wn WC-->Major O+ nts=4 GGGG A.G41,A.G45,A.G50,A.G54
  step#1  pm(>>,forward)  area=9.93  rise=3.51 twist=29.1
  strand#1  U RNA glyco-bond=-- sugar=-- nts=2 GG A.G40,A.G41
  strand#2  U RNA glyco-bond=-- sugar=33 nts=2 GG A.G44,A.G45
  strand#3  U RNA glyco-bond=-- sugar=3- nts=2 GG A.G49,A.G50
  strand#4* D RNA glyco-bond=ss sugar=-3 nts=2 GG A.G56,A.G54 bulged-nts=1 U A.U55
  loop#1 type=propeller strands=[#1,#2] nts=2 AA A.A42,A.A43
  loop#2 type=propeller strands=[#2,#3] nts=3 UUU A.U46,A.U47,A.U48
  loop#3 type=lateral   strands=[#3,#4] nts=3 UAU A.U51,A.A52,A.U53

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