Summary information

PDB id
8x0s
Class
RNA
Method
X-ray (2.956 Å)
Summary
Crystal structure of r(g4c2)2
Reference
Geng Y, Liu C, Xu N, Suen MC, Miao H, Xie Y, Zhang B, Chen X, Song Y, Wang Z, Cai Q, Zhu G (2024): "Crystal structure of a tetrameric RNA G-quadruplex formed by hexanucleotide repeat expansions of C9orf72 in ALS/FTD." Nucleic Acids Res., 52, 7961-7970. doi: 10.1093/nar/gkae473.
Abstract
The abnormal GGGGCC hexanucleotide repeat expansions (HREs) in C9orf72 cause the fatal neurodegenerative diseases including amyotrophic lateral sclerosis and frontotemporal dementia. The transcribed RNA HREs, short for r(G4C2)n, can form toxic RNA foci which sequestrate RNA binding proteins and impair RNA processing, ultimately leading to neurodegeneration. Here, we determined the crystal structure of r(G4C2)2, which folds into a parallel tetrameric G-quadruplex composed of two four-layer dimeric G-quadruplex via 5'-to-5' stacking in coordination with a K+ ion. Notably, the two C bases locate at 3'- end stack on the outer G-tetrad with the assistance of two additional K+ ions. The high-resolution structure reported here lays a foundation in understanding the mechanism of neurological toxicity of RNA HREs. Furthermore, the atomic details provide a structural basis for the development of potential therapeutic agents against the fatal neurodegenerative diseases ALS/FTD.
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

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List of 8 G-tetrads

 1 glyco-bond=---- sugar=3-3- groove=---- planarity=0.151 type=planar nts=4 GGGG 1:A.G1,1:A.G7,2:A.G1,2:A.G7
 2 glyco-bond=---- sugar=3333 groove=---- planarity=0.167 type=other  nts=4 GGGG 1:A.G2,1:A.G8,2:A.G2,2:A.G8
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.161 type=other  nts=4 GGGG 1:A.G3,1:A.G9,2:A.G3,2:A.G9
 4 glyco-bond=---- sugar=-3-3 groove=---- planarity=0.101 type=planar nts=4 GGGG 1:A.G4,1:A.G10,2:A.G4,2:A.G10
 5 glyco-bond=---- sugar=3-3- groove=---- planarity=0.164 type=other  nts=4 GGGG 1:B.G1,1:B.G7,2:B.G1,2:B.G7
 6 glyco-bond=---- sugar=3333 groove=---- planarity=0.187 type=other  nts=4 GGGG 1:B.G2,1:B.G8,2:B.G2,2:B.G8
 7 glyco-bond=---- sugar=---- groove=---- planarity=0.134 type=planar nts=4 GGGG 1:B.G3,1:B.G9,2:B.G3,2:B.G9
 8 glyco-bond=---- sugar=-3-3 groove=---- planarity=0.070 type=planar nts=4 GGGG 1:B.G4,1:B.G10,2:B.G4,2:B.G10

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

 1  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GGGG 1:A.G4,1:A.G10,2:A.G4,2:A.G10
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:A.G3,1:A.G9,2:A.G3,2:A.G9
 3  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:A.G2,1:A.G8,2:A.G2,2:A.G8
 4* glyco-bond=---- sugar=3-3- groove=---- WC-->Major nts=4 GGGG 1:A.G1,1:A.G7,2:A.G1,2:A.G7
 5  glyco-bond=---- sugar=-3-3 groove=---- Major-->WC nts=4 GGGG 2:B.G7,2:B.G1,1:B.G7,1:B.G1
 6  glyco-bond=---- sugar=3333 groove=---- Major-->WC nts=4 GGGG 2:B.G8,2:B.G2,1:B.G8,1:B.G2
 7  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG 2:B.G9,2:B.G3,1:B.G9,1:B.G3
 8  glyco-bond=---- sugar=3-3- groove=---- Major-->WC nts=4 GGGG 2:B.G10,2:B.G4,1:B.G10,1:B.G4
  step#1  mp(<<,backward) area=7.17  rise=3.23 twist=35.6
  step#2  mp(<<,backward) area=15.26 rise=3.71 twist=20.8
  step#3  mp(<<,backward) area=8.67  rise=3.28 twist=33.6
  step#4  mm(<>,outward)  area=8.74  rise=3.35 twist=25.9
  step#5  pm(>>,forward)  area=8.83  rise=3.28 twist=33.5
  step#6  pm(>>,forward)  area=15.71 rise=3.71 twist=20.3
  step#7  pm(>>,forward)  area=7.14  rise=3.23 twist=35.3
  strand#1 RNA glyco-bond=-------- sugar=--33-3-3 nts=8 GGGGGGGG 1:A.G4,1:A.G3,1:A.G2,1:A.G1,2:B.G7,2:B.G8,2:B.G9,2:B.G10
  strand#2 RNA glyco-bond=-------- sugar=3-3-33-- nts=8 GGGGGGGG 1:A.G10,1:A.G9,1:A.G8,1:A.G7,2:B.G1,2:B.G2,2:B.G3,2:B.G4
  strand#3 RNA glyco-bond=-------- sugar=--33-3-3 nts=8 GGGGGGGG 2:A.G4,2:A.G3,2:A.G2,2:A.G1,1:B.G7,1:B.G8,1:B.G9,1:B.G10
  strand#4 RNA glyco-bond=-------- sugar=3-3-33-- nts=8 GGGGGGGG 2:A.G10,2:A.G9,2:A.G8,2:A.G7,1:B.G1,1:B.G2,1:B.G3,1:B.G4

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7 stacking diagrams 
 1  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GGGG 1:A.G4,1:A.G10,2:A.G4,2:A.G10
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:A.G3,1:A.G9,2:A.G3,2:A.G9
  step#1  mp(<<,backward) area=7.17  rise=3.23 twist=35.6

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 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:A.G3,1:A.G9,2:A.G3,2:A.G9
 3  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:A.G2,1:A.G8,2:A.G2,2:A.G8
  step#2  mp(<<,backward) area=15.26 rise=3.71 twist=20.8

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 3  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:A.G2,1:A.G8,2:A.G2,2:A.G8
 4* glyco-bond=---- sugar=3-3- groove=---- WC-->Major nts=4 GGGG 1:A.G1,1:A.G7,2:A.G1,2:A.G7
  step#3  mp(<<,backward) area=8.67  rise=3.28 twist=33.6

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 4* glyco-bond=---- sugar=3-3- groove=---- WC-->Major nts=4 GGGG 1:A.G1,1:A.G7,2:A.G1,2:A.G7
 5  glyco-bond=---- sugar=-3-3 groove=---- Major-->WC nts=4 GGGG 2:B.G7,2:B.G1,1:B.G7,1:B.G1
  step#4  mm(<>,outward)  area=8.74  rise=3.35 twist=25.9

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 5  glyco-bond=---- sugar=-3-3 groove=---- Major-->WC nts=4 GGGG 2:B.G7,2:B.G1,1:B.G7,1:B.G1
 6  glyco-bond=---- sugar=3333 groove=---- Major-->WC nts=4 GGGG 2:B.G8,2:B.G2,1:B.G8,1:B.G2
  step#5  pm(>>,forward)  area=8.83  rise=3.28 twist=33.5

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 6  glyco-bond=---- sugar=3333 groove=---- Major-->WC nts=4 GGGG 2:B.G8,2:B.G2,1:B.G8,1:B.G2
 7  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG 2:B.G9,2:B.G3,1:B.G9,1:B.G3
  step#6  pm(>>,forward)  area=15.71 rise=3.71 twist=20.3

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 7  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG 2:B.G9,2:B.G3,1:B.G9,1:B.G3
 8  glyco-bond=---- sugar=3-3- groove=---- Major-->WC nts=4 GGGG 2:B.G10,2:B.G4,1:B.G10,1:B.G4
  step#7  pm(>>,forward)  area=7.14  rise=3.23 twist=35.3

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

 1  glyco-bond=---- sugar=3-3- groove=---- WC-->Major nts=4 GGGG 1:A.G1,1:A.G7,2:A.G1,2:A.G7
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:A.G2,1:A.G8,2:A.G2,2:A.G8
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:A.G3,1:A.G9,2:A.G3,2:A.G9
 4  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GGGG 1:A.G4,1:A.G10,2:A.G4,2:A.G10
  step#1  pm(>>,forward)  area=8.67  rise=3.28 twist=33.6
  step#2  pm(>>,forward)  area=15.26 rise=3.71 twist=20.8
  step#3  pm(>>,forward)  area=7.17  rise=3.23 twist=35.6
  strand#1  U RNA glyco-bond=---- sugar=33-- nts=4 GGGG 1:A.G1,1:A.G2,1:A.G3,1:A.G4
  strand#2  U RNA glyco-bond=---- sugar=-3-3 nts=4 GGGG 1:A.G7,1:A.G8,1:A.G9,1:A.G10
  strand#3  U RNA glyco-bond=---- sugar=33-- nts=4 GGGG 2:A.G1,2:A.G2,2:A.G3,2:A.G4
  strand#4  U RNA glyco-bond=---- sugar=-3-3 nts=4 GGGG 2:A.G7,2:A.G8,2:A.G9,2:A.G10
  loop#1 type=propeller strands=[#1,#2] nts=2 CC 1:A.C5,1:A.C6
  loop#2 type=propeller strands=[#3,#4] nts=2 CC 2:A.C5,2:A.C6

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

 1  glyco-bond=---- sugar=3-3- groove=---- WC-->Major nts=4 GGGG 1:B.G1,1:B.G7,2:B.G1,2:B.G7
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:B.G2,1:B.G8,2:B.G2,2:B.G8
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:B.G3,1:B.G9,2:B.G3,2:B.G9
 4  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GGGG 1:B.G4,1:B.G10,2:B.G4,2:B.G10
  step#1  pm(>>,forward)  area=8.83  rise=3.28 twist=33.5
  step#2  pm(>>,forward)  area=15.71 rise=3.71 twist=20.3
  step#3  pm(>>,forward)  area=7.14  rise=3.23 twist=35.3
  strand#1  U RNA glyco-bond=---- sugar=33-- nts=4 GGGG 1:B.G1,1:B.G2,1:B.G3,1:B.G4
  strand#2  U RNA glyco-bond=---- sugar=-3-3 nts=4 GGGG 1:B.G7,1:B.G8,1:B.G9,1:B.G10
  strand#3  U RNA glyco-bond=---- sugar=33-- nts=4 GGGG 2:B.G1,2:B.G2,2:B.G3,2:B.G4
  strand#4  U RNA glyco-bond=---- sugar=-3-3 nts=4 GGGG 2:B.G7,2:B.G8,2:B.G9,2:B.G10
  loop#1 type=propeller strands=[#1,#2] nts=2 CC 1:B.C5,1:B.C6
  loop#2 type=propeller strands=[#3,#4] nts=2 CC 2:B.C5,2:B.C6

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List of 1 G4 coaxial stack

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