Summary information [schematics · tetrads · helices · stems · costacks · homepage]

PDB-id
2n21
Class
hydrolase-DNA
Method
NMR
Summary
Solution structure of complex between DNA G-quadruplex and G-quadruplex recognition domain of rhau
Reference
Heddi, B., Cheong, V.V., Martadinata, H., Phan, A.T.: (2015) "Insights into G-quadruplex specific recognition by the DEAH-box helicase RHAU: Solution structure of a peptide-quadruplex complex." Proc.Natl.Acad.Sci.USA
Abstract
Four-stranded nucleic acid structures called G-quadruplexes have been associated with important cellular processes, which should require G-quadruplex-protein interaction. However, the structural basis for specific G-quadruplex recognition by proteins has not been understood. The DEAH (Asp-Glu-Ala-His) box RNA helicase associated with AU-rich element (RHAU) (also named DHX36 or G4R1) specifically binds to and resolves parallel-stranded G-quadruplexes. Here we identified an 18-amino acid G-quadruplex-binding domain of RHAU and determined the structure of this peptide bound to a parallel DNA G-quadruplex. Our structure explains how RHAU specifically recognizes parallel G-quadruplexes. The peptide covers a terminal guanine base tetrad (G-tetrad), and clamps the G-quadruplex using three-anchor-point electrostatic interactions between three positively charged amino acids and negatively charged phosphate groups. This binding mode is strikingly similar to that of most ligands selected for specific G-quadruplex targeting. Binding to an exposed G-tetrad represents a simple and efficient way to specifically target G-quadruplex structures.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · 3(-P-P-P), parallel(4+0), UUUU

Base-block schematics in six views [summary · tetrads · helices · stems · costacks · homepage]

PyMOL session file PDB file View in 3Dmol.js

List of 3 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=---- groove=---- planarity=0.225 type=other  nts=4 GGGG B.DG3,B.DG7,B.DG11,B.DG15
 2 glyco-bond=---- groove=---- planarity=0.150 type=planar nts=4 GGGG B.DG4,B.DG8,B.DG12,B.DG16
 3 glyco-bond=---- groove=---- planarity=0.194 type=other  nts=4 GGGG B.DG5,B.DG9,B.DG13,B.DG17

List of 1 G4-helix [summary · schematics · tetrads · stems · costacks · homepage]

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-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG7,B.DG11,B.DG15
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG4,B.DG8,B.DG12,B.DG16
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG5,B.DG9,B.DG13,B.DG17
  step#1  pm(>>,forward)  area=9.62  rise=3.35 twist=33.8
  step#2  pm(>>,forward)  area=14.15 rise=3.35 twist=31.4
  strand#1 DNA glyco-bond=--- nts=3 GGG B.DG3,B.DG4,B.DG5
  strand#2 DNA glyco-bond=--- nts=3 GGG B.DG7,B.DG8,B.DG9
  strand#3 DNA glyco-bond=--- nts=3 GGG B.DG11,B.DG12,B.DG13
  strand#4 DNA glyco-bond=--- nts=3 GGG B.DG15,B.DG16,B.DG17

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2 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG7,B.DG11,B.DG15
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG4,B.DG8,B.DG12,B.DG16
step#1 pm(>>,forward) area=9.62 rise=3.35 twist=33.8

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG4,B.DG8,B.DG12,B.DG16
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG5,B.DG9,B.DG13,B.DG17
step#2 pm(>>,forward) area=14.15 rise=3.35 twist=31.4

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List of 1 G4-stem [summary · schematics · tetrads · helices · costacks · homepage]

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-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 3(-P-P-P), parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG7,B.DG11,B.DG15
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG4,B.DG8,B.DG12,B.DG16
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG5,B.DG9,B.DG13,B.DG17
  step#1  pm(>>,forward)  area=9.62  rise=3.35 twist=33.8
  step#2  pm(>>,forward)  area=14.15 rise=3.35 twist=31.4
  strand#1  U DNA glyco-bond=--- nts=3 GGG B.DG3,B.DG4,B.DG5
  strand#2  U DNA glyco-bond=--- nts=3 GGG B.DG7,B.DG8,B.DG9
  strand#3  U DNA glyco-bond=--- nts=3 GGG B.DG11,B.DG12,B.DG13
  strand#4  U DNA glyco-bond=--- nts=3 GGG B.DG15,B.DG16,B.DG17
  loop#1 type=propeller strands=[#1,#2] nts=1 T B.DT6
  loop#2 type=propeller strands=[#2,#3] nts=1 T B.DT10
  loop#3 type=propeller strands=[#3,#4] nts=1 T B.DT14

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List of 0 G4 coaxial stacks [summary · schematics · tetrads · helices · stems · homepage]

List of 0 non-stem G4-loops (including the two closing Gs)