Summary information and primary citation

PDB-id
8vvd
Class
motor protein-RNA
Method
cryo-EM (3.0 Å)
Summary
cryo-EM structure of dhx36 bound to a RNA g-quadruplex derived from the cmyc g-quadruplex, class 2
Reference
Banco MT, Paul T, Jiang J, Myong S, Ferre-D'Amare AR: "Inter-domain synergy enables both DNA and RNA G-quadruplex unwinding by the DEAH-box helicase DHX36."
Abstract
 
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, UUUU, parallel, 4+0,

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

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List of 3 G-tetrads

 1 glyco-bond=---- sugar=33-- groove=---- planarity=0.131 type=planar O+ nts=4 GGGG B.G2,B.G6,B.G11,B.G15
 2 glyco-bond=---- sugar=3333 groove=---- planarity=0.131 type=planar O+ nts=4 GGGG B.G3,B.G7,B.G12,B.G16
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.429 type=bowl   O+ nts=4 GGGG B.G4,B.G8,B.G13,B.G17

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-tetrads, INTRA-molecular, with 1 stem
 1  glyco-bond=---- sugar=33-- groove=---- WC-->Major O+ nts=4 GGGG B.G2,B.G6,B.G11,B.G15
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG B.G3,B.G7,B.G12,B.G16
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG B.G4,B.G8,B.G13,B.G17
  step#1  pm(>>,forward)  area=7.74  rise=3.21 twist=34.6
  step#2  pm(>>,forward)  area=14.79 rise=3.69 twist=23.7
  strand#1 RNA glyco-bond=--- sugar=33- nts=3 GGG B.G2,B.G3,B.G4
  strand#2 RNA glyco-bond=--- sugar=33- nts=3 GGG B.G6,B.G7,B.G8
  strand#3 RNA glyco-bond=--- sugar=-3- nts=3 GGG B.G11,B.G12,B.G13
  strand#4 RNA glyco-bond=--- sugar=-3- nts=3 GGG B.G15,B.G16,B.G17

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2 stacking diagrams 
 1  glyco-bond=---- sugar=33-- groove=---- WC-->Major O+ nts=4 GGGG B.G2,B.G6,B.G11,B.G15
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG B.G3,B.G7,B.G12,B.G16
  step#1  pm(>>,forward)  area=7.74  rise=3.21 twist=34.6

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 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG B.G3,B.G7,B.G12,B.G16
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG B.G4,B.G8,B.G13,B.G17
  step#2  pm(>>,forward)  area=14.79 rise=3.69 twist=23.7

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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, 3 G-tetrads, 0 loops, INTRA-molecular, UUUU, parallel, 4+0, descriptor
 1  glyco-bond=---- sugar=33-- groove=---- WC-->Major O+ nts=4 GGGG B.G2,B.G6,B.G11,B.G15
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG B.G3,B.G7,B.G12,B.G16
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG B.G4,B.G8,B.G13,B.G17
  step#1  pm(>>,forward)  area=7.74  rise=3.21 twist=34.6
  step#2  pm(>>,forward)  area=14.79 rise=3.69 twist=23.7
  strand#1  U RNA glyco-bond=--- sugar=33- nts=3 GGG B.G2,B.G3,B.G4
  strand#2  U RNA glyco-bond=--- sugar=33- nts=3 GGG B.G6,B.G7,B.G8
  strand#3  U RNA glyco-bond=--- sugar=-3- nts=3 GGG B.G11,B.G12,B.G13
  strand#4  U RNA glyco-bond=--- sugar=-3- nts=3 GGG B.G15,B.G16,B.G17

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