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PDB-id
2m18
Class
RNA
Method
NMR
Summary
Structure of stacked G-quadruplex formed by human terra sequence in potassium solution
Reference
Martadinata, H., Phan, A.T.: (2013) "Structure of Human Telomeric RNA (TERRA): Stacking of Two G-Quadruplex Blocks in K(+) Solution." Biochemistry, 52, 2176-2183.
Abstract
Telomeric repeat-containing RNAs (TERRA) are transcription products of the telomeres. Human TERRA sequences containing UUAGGG repeats can form parallel-stranded G-quadruplexes. The stacking interaction of such structures was shown to be important for ligand targeting and higher-order arrangement of G-quadruplexes in long TERRA sequences. Here we report on the first high-resolution structure of a stacked G-quadruplex formed by the 10-nucleotide human TERRA sequence r(GGGUUAGGGU) in potassium solution. This structure comprises two dimeric three-layer parallel-stranded G-quadruplex blocks, which stack on each other at their 5'-ends. The adenine in each UUA loop is nearly coplanar with the 5'-end G-tetrad forming an A·(G·G·G·G)·A hexad, thereby increasing the stacking contacts between the two blocks. Interestingly, this stacking and loop conformation is different from all structures previously reported for the free human TERRA but resembles the structure previously determined for a complex between a human TERRA sequence and an acridine ligand. This stacking conformation is a potential target for drugs that recognize or induce the stacking interface.
G4 notes
6 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 6 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=---- groove=---- planarity=0.494 type=other  nts=4 GGGG A.G1,A.G7,B.G11,B.G17
 2 glyco-bond=---- groove=---- planarity=0.419 type=saddle nts=4 GGGG A.G2,A.G8,B.G12,B.G18
 3 glyco-bond=---- groove=---- planarity=0.432 type=other  nts=4 GGGG A.G3,A.G9,B.G13,B.G19
 4 glyco-bond=---- groove=---- planarity=0.494 type=other  nts=4 GGGG C.G21,C.G27,D.G31,D.G37
 5 glyco-bond=---- groove=---- planarity=0.487 type=other  nts=4 GGGG C.G22,C.G28,D.G32,D.G38
 6 glyco-bond=---- groove=---- planarity=0.498 type=other  nts=4 GGGG C.G23,C.G29,D.G33,D.G39

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G3,A.G9,B.G13,B.G19
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G2,A.G8,B.G12,B.G18
 3* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G1,A.G7,B.G11,B.G17
 4  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG D.G31,C.G27,C.G21,D.G37
 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG D.G32,C.G28,C.G22,D.G38
 6  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG D.G33,C.G29,C.G23,D.G39
  step#1  mp(<<,backward) area=16.77 rise=3.46 twist=28.5
  step#2  mp(<<,backward) area=19.82 rise=3.76 twist=23.3
  step#3  mm(<>,outward)  area=9.84  rise=3.50 twist=-60.5
  step#4  pm(>>,forward)  area=19.75 rise=3.70 twist=23.9
  step#5  pm(>>,forward)  area=17.59 rise=3.48 twist=27.3
  strand#1 RNA glyco-bond=------ nts=6 GGGGGG A.G3,A.G2,A.G1,D.G31,D.G32,D.G33
  strand#2 RNA glyco-bond=------ nts=6 GGGGGG A.G9,A.G8,A.G7,C.G27,C.G28,C.G29
  strand#3 RNA glyco-bond=------ nts=6 GGGGGG B.G13,B.G12,B.G11,C.G21,C.G22,C.G23
  strand#4 RNA glyco-bond=------ nts=6 GGGGGG B.G19,B.G18,B.G17,D.G37,D.G38,D.G39

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5 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G3,A.G9,B.G13,B.G19
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G2,A.G8,B.G12,B.G18
step#1 mp(<<,backward) area=16.77 rise=3.46 twist=28.5

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G2,A.G8,B.G12,B.G18
3* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G1,A.G7,B.G11,B.G17
step#2 mp(<<,backward) area=19.82 rise=3.76 twist=23.3

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 3* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G1,A.G7,B.G11,B.G17
4 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG D.G31,C.G27,C.G21,D.G37
step#3 mm(<>,outward) area=9.84 rise=3.50 twist=-60.5

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 4  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG D.G31,C.G27,C.G21,D.G37
5 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG D.G32,C.G28,C.G22,D.G38
step#4 pm(>>,forward) area=19.75 rise=3.70 twist=23.9

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 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG D.G32,C.G28,C.G22,D.G38
6 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG D.G33,C.G29,C.G23,D.G39
step#5 pm(>>,forward) area=17.59 rise=3.48 twist=27.3

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G1,A.G7,B.G11,B.G17
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G2,A.G8,B.G12,B.G18
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.G3,A.G9,B.G13,B.G19
  step#1  pm(>>,forward)  area=19.82 rise=3.76 twist=23.3
  step#2  pm(>>,forward)  area=16.77 rise=3.46 twist=28.5
  strand#1  U RNA glyco-bond=--- nts=3 GGG A.G1,A.G2,A.G3
  strand#2  U RNA glyco-bond=--- nts=3 GGG A.G7,A.G8,A.G9
  strand#3  U RNA glyco-bond=--- nts=3 GGG B.G11,B.G12,B.G13
  strand#4  U RNA glyco-bond=--- nts=3 GGG B.G17,B.G18,B.G19
  loop#1 type=propeller strands=[#1,#2] nts=3 UUA A.U4,A.U5,A.A6
  loop#2 type=propeller strands=[#3,#4] nts=3 UUA B.U14,B.U15,B.A16

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Stem#2, 3 G-tetrad layers, 2 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG C.G21,C.G27,D.G31,D.G37
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG C.G22,C.G28,D.G32,D.G38
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG C.G23,C.G29,D.G33,D.G39
  step#1  pm(>>,forward)  area=19.75 rise=3.70 twist=23.9
  step#2  pm(>>,forward)  area=17.59 rise=3.48 twist=27.3
  strand#1  U RNA glyco-bond=--- nts=3 GGG C.G21,C.G22,C.G23
  strand#2  U RNA glyco-bond=--- nts=3 GGG C.G27,C.G28,C.G29
  strand#3  U RNA glyco-bond=--- nts=3 GGG D.G31,D.G32,D.G33
  strand#4  U RNA glyco-bond=--- nts=3 GGG D.G37,D.G38,D.G39
  loop#1 type=propeller strands=[#1,#2] nts=3 UUA C.U24,C.U25,C.A26
  loop#2 type=propeller strands=[#3,#4] nts=3 UUA D.U34,D.U35,D.A36

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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)