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

PDB-id
4xk0*
Class
RNA
Method
X-ray (1.08 Å)
Summary
Crystal structure of a tetramolecular RNA G-quadruplex in potassium
Reference
Chen, M.C., Murat, P., Abecassis, K., Ferre-D'Amare, A.R., Balasubramanian, S.: (2015) "Insights into the mechanism of a G-quadruplex-unwinding DEAH-box helicase." Nucleic Acids Res., 43, 2223-2231.
Abstract
The unwinding of nucleic acid secondary structures within cells is crucial to maintain genomic integrity and prevent abortive transcription and translation initiation. DHX36, also known as RHAU or G4R1, is a DEAH-box ATP-dependent helicase highly specific for DNA and RNA G-quadruplexes (G4s). A fundamental mechanistic understanding of the interaction between helicases and their G4 substrates is important to elucidate G4 biology and pave the way toward G4-targeted therapies. Here we analyze how the thermodynamic stability of G4 substrates affects binding and unwinding by DHX36. We modulated the stability of the G4 substrates by varying the sequence and the number of G-tetrads and by using small, G4-stabilizing molecules. We found an inverse correlation between the thermodynamic stability of the G4 substrates and rates of unwinding by DHX36. In stark contrast, the ATPase activity of the helicase was largely independent of substrate stability pointing toward a decoupling mechanism akin to what has been observed for many double-stranded DEAD-box RNA helicases. Our study provides the first evidence that DHX36 uses a local, non-processive mechanism to unwind G4 substrates, reminiscent of that of eukaryotic initiation factor 4A (eIF4A) on double-stranded substrates.
G4 notes
8 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack · parallel(4+0), UUUU · coaxial interfaces: 5'/5'

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

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List of 8 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=---- groove=---- planarity=0.385 type=bowl   nts=4 GGGG 1:A.G1,4:A.G1,2:A.G1,3:A.G1
 2 glyco-bond=---- groove=---- planarity=0.105 type=planar nts=4 GGGG 1:A.G2,4:A.G2,2:A.G2,3:A.G2
 3 glyco-bond=---- groove=---- planarity=0.109 type=planar nts=4 GGGG 1:A.G3,4:A.G3,2:A.G3,3:A.G3
 4 glyco-bond=---- groove=---- planarity=0.223 type=bowl   nts=4 GGGG 1:A.G4,4:A.G4,2:A.G4,3:A.G4
 5 glyco-bond=---- groove=---- planarity=0.170 type=other  nts=4 GGGG 1:C.G-2,3:C.G-2,2:C.G-2,4:C.G-2
 6 glyco-bond=---- groove=---- planarity=0.171 type=other  nts=4 GGGG 1:C.G-1,3:C.G-1,2:C.G-1,4:C.G-1
 7 glyco-bond=---- groove=---- planarity=0.134 type=planar nts=4 GGGG 1:C.G0,3:C.G0,2:C.G0,4:C.G0
 8 glyco-bond=---- groove=---- planarity=0.246 type=bowl   nts=4 GGGG 1:C.G1,3:C.G1,2:C.G1,4:C.G1

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, 8 G-tetrad layers, inter-molecular, with 2 stems

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G4,4:A.G4,2:A.G4,3:A.G4
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G3,4:A.G3,2:A.G3,3:A.G3
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G2,4:A.G2,2:A.G2,3:A.G2
 4* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G1,4:A.G1,2:A.G1,3:A.G1
 5  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:C.G-2,3:C.G-2,2:C.G-2,4:C.G-2
 6  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:C.G-1,3:C.G-1,2:C.G-1,4:C.G-1
 7  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:C.G0,3:C.G0,2:C.G0,4:C.G0
 8  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:C.G1,3:C.G1,2:C.G1,4:C.G1
  step#1  mp(<<,backward) area=13.32 rise=3.61 twist=24.6
  step#2  mp(<<,backward) area=9.01  rise=3.29 twist=33.6
  step#3  mp(<<,backward) area=7.27  rise=3.20 twist=35.7
  step#4  mm(<>,outward)  area=25.60 rise=3.59 twist=84.4
  step#5  pm(>>,forward)  area=12.93 rise=3.41 twist=29.5
  step#6  pm(>>,forward)  area=10.90 rise=3.43 twist=30.9
  step#7  pm(>>,forward)  area=13.55 rise=3.68 twist=23.9
  strand#1 RNA glyco-bond=-------- nts=8 GGGGGGGG 1:A.G4,1:A.G3,1:A.G2,1:A.G1,1:C.G-2,1:C.G-1,1:C.G0,1:C.G1
  strand#2 RNA glyco-bond=-------- nts=8 GGGGGGGG 4:A.G4,4:A.G3,4:A.G2,4:A.G1,3:C.G-2,3:C.G-1,3:C.G0,3:C.G1
  strand#3 RNA glyco-bond=-------- nts=8 GGGGGGGG 2:A.G4,2:A.G3,2:A.G2,2:A.G1,2:C.G-2,2:C.G-1,2:C.G0,2:C.G1
  strand#4 RNA glyco-bond=-------- nts=8 GGGGGGGG 3:A.G4,3:A.G3,3:A.G2,3:A.G1,4:C.G-2,4:C.G-1,4:C.G0,4:C.G1

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7 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G4,4:A.G4,2:A.G4,3:A.G4
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G3,4:A.G3,2:A.G3,3:A.G3
step#1 mp(<<,backward) area=13.32 rise=3.61 twist=24.6

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G3,4:A.G3,2:A.G3,3:A.G3
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G2,4:A.G2,2:A.G2,3:A.G2
step#2 mp(<<,backward) area=9.01 rise=3.29 twist=33.6

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 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G2,4:A.G2,2:A.G2,3:A.G2
4* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G1,4:A.G1,2:A.G1,3:A.G1
step#3 mp(<<,backward) area=7.27 rise=3.20 twist=35.7

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 4* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G1,4:A.G1,2:A.G1,3:A.G1
5 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:C.G-2,3:C.G-2,2:C.G-2,4:C.G-2
step#4 mm(<>,outward) area=25.60 rise=3.59 twist=84.4

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 5  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:C.G-2,3:C.G-2,2:C.G-2,4:C.G-2
6 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:C.G-1,3:C.G-1,2:C.G-1,4:C.G-1
step#5 pm(>>,forward) area=12.93 rise=3.41 twist=29.5

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 6  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:C.G-1,3:C.G-1,2:C.G-1,4:C.G-1
7 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:C.G0,3:C.G0,2:C.G0,4:C.G0
step#6 pm(>>,forward) area=10.90 rise=3.43 twist=30.9

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 7  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:C.G0,3:C.G0,2:C.G0,4:C.G0
8 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:C.G1,3:C.G1,2:C.G1,4:C.G1
step#7 pm(>>,forward) area=13.55 rise=3.68 twist=23.9

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List of 2 G4-stems [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, 4 G-tetrad layers, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G1,4:A.G1,2:A.G1,3:A.G1
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G2,4:A.G2,2:A.G2,3:A.G2
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G3,4:A.G3,2:A.G3,3:A.G3
 4  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G4,4:A.G4,2:A.G4,3:A.G4
  step#1  pm(>>,forward)  area=7.27  rise=3.20 twist=35.7
  step#2  pm(>>,forward)  area=9.01  rise=3.29 twist=33.6
  step#3  pm(>>,forward)  area=13.32 rise=3.61 twist=24.6
  strand#1  U RNA glyco-bond=---- nts=4 GGGG 1:A.G1,1:A.G2,1:A.G3,1:A.G4
  strand#2  U RNA glyco-bond=---- nts=4 GGGG 4:A.G1,4:A.G2,4:A.G3,4:A.G4
  strand#3  U RNA glyco-bond=---- nts=4 GGGG 2:A.G1,2:A.G2,2:A.G3,2:A.G4
  strand#4  U RNA glyco-bond=---- nts=4 GGGG 3:A.G1,3:A.G2,3:A.G3,3:A.G4

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Stem#2, 4 G-tetrad layers, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:C.G-2,3:C.G-2,2:C.G-2,4:C.G-2
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:C.G-1,3:C.G-1,2:C.G-1,4:C.G-1
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:C.G0,3:C.G0,2:C.G0,4:C.G0
 4  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:C.G1,3:C.G1,2:C.G1,4:C.G1
  step#1  pm(>>,forward)  area=12.93 rise=3.41 twist=29.5
  step#2  pm(>>,forward)  area=10.90 rise=3.43 twist=30.9
  step#3  pm(>>,forward)  area=13.55 rise=3.68 twist=23.9
  strand#1  U RNA glyco-bond=---- nts=4 GGGG 1:C.G-2,1:C.G-1,1:C.G0,1:C.G1
  strand#2  U RNA glyco-bond=---- nts=4 GGGG 3:C.G-2,3:C.G-1,3:C.G0,3:C.G1
  strand#3  U RNA glyco-bond=---- nts=4 GGGG 2:C.G-2,2:C.G-1,2:C.G0,2:C.G1
  strand#4  U RNA glyco-bond=---- nts=4 GGGG 4:C.G-2,4:C.G-1,4:C.G0,4:C.G1

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List of 1 G4 coaxial stack [summary · schematics · tetrads · helices · stems · homepage]

 1 G4 helix#1 contains 2 G4 stems: [#1,#2]  [5'/5']

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