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

PDB-id
6jjh*
Class
RNA
Method
X-ray (1.74 Å)
Summary
Crystal structure of a two-quartet RNA parallel G-quadruplex complexed with the porphyrin tmpyp4
Reference
Zhang, Y.S., EI Omari, K., Duman, R., Wagner, A., Parkinson, G.N., Wei, D.G.: "Crystal structure of a two-quartet RNA parallel G-quadruplex complexed with the porphyrin TMPyP4." To be published
Abstract
 
G4 notes
4 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack · parallel(4+0), UUUU · coaxial interfaces: 3'/5'

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

PyMOL session file PDB file View in 3Dmol.js

List of 4 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=ssss groove=---- planarity=0.103 type=planar nts=4 GGGG 1:B.G1,2:B.G6,2:B.G1,1:B.G6
 2 glyco-bond=---- groove=---- planarity=0.127 type=planar nts=4 GGGG 1:B.G2,1:B.G7,2:B.G2,2:B.G7
 3 glyco-bond=---- groove=---- planarity=0.124 type=planar nts=4 GGGG 1:B.G9,1:B.G12,2:B.G9,2:B.G12
 4 glyco-bond=---- groove=---- planarity=0.063 type=planar nts=4 GGGG 1:B.G10,1:B.G13,2:B.G10,2:B.G13

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

 1  glyco-bond=ssss groove=---- Major-->WC nts=4 GGGG 1:B.G1,2:B.G6,2:B.G1,1:B.G6
 2* glyco-bond=---- groove=---- Major-->WC nts=4 GGGG 1:B.G2,2:B.G7,2:B.G2,1:B.G7
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:B.G12,2:B.G9,2:B.G12,1:B.G9
 4  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:B.G13,2:B.G10,2:B.G13,1:B.G10
  step#1  mp(<<,backward) area=5.95  rise=3.25 twist=-45.7
  step#2  mm(<>,outward)  area=27.96 rise=3.38 twist=-8.3
  step#3  pm(>>,forward)  area=10.34 rise=3.35 twist=31.4
  strand#1 RNA glyco-bond=s--- nts=4 GGGG 1:B.G1,1:B.G2,1:B.G12,1:B.G13
  strand#2 RNA glyco-bond=s--- nts=4 GGGG 2:B.G6,2:B.G7,2:B.G9,2:B.G10
  strand#3 RNA glyco-bond=s--- nts=4 GGGG 2:B.G1,2:B.G2,2:B.G12,2:B.G13
  strand#4 RNA glyco-bond=s--- nts=4 GGGG 1:B.G6,1:B.G7,1:B.G9,1:B.G10

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3 stacking diagrams
 1  glyco-bond=ssss groove=---- Major-->WC nts=4 GGGG 1:B.G1,2:B.G6,2:B.G1,1:B.G6
2* glyco-bond=---- groove=---- Major-->WC nts=4 GGGG 1:B.G2,2:B.G7,2:B.G2,1:B.G7
step#1 mp(<<,backward) area=5.95 rise=3.25 twist=-45.7

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 2* glyco-bond=---- groove=---- Major-->WC nts=4 GGGG 1:B.G2,2:B.G7,2:B.G2,1:B.G7
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:B.G12,2:B.G9,2:B.G12,1:B.G9
step#2 mm(<>,outward) area=27.96 rise=3.38 twist=-8.3

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 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:B.G12,2:B.G9,2:B.G12,1:B.G9
4 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:B.G13,2:B.G10,2:B.G13,1:B.G10
step#3 pm(>>,forward) area=10.34 rise=3.35 twist=31.4

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

 1  glyco-bond=ssss groove=---- Major-->WC nts=4 GGGG 1:B.G1,2:B.G6,2:B.G1,1:B.G6
 2  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG 1:B.G2,2:B.G7,2:B.G2,1:B.G7
  step#1  mp(<<,backward) area=5.95  rise=3.25 twist=-45.7
  strand#1  U RNA glyco-bond=s- nts=2 GG 1:B.G1,1:B.G2
  strand#2  U RNA glyco-bond=s- nts=2 GG 2:B.G6,2:B.G7
  strand#3  U RNA glyco-bond=s- nts=2 GG 2:B.G1,2:B.G2
  strand#4  U RNA glyco-bond=s- nts=2 GG 1:B.G6,1:B.G7
  loop#1 type=propeller strands=[#1,#4] nts=3 CUC 1:B.C3,1:B.U4,1:B.C5
  loop#2 type=propeller strands=[#3,#2] nts=3 CUC 2:B.C3,2:B.U4,2:B.C5

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:B.G9,1:B.G12,2:B.G9,2:B.G12
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:B.G10,1:B.G13,2:B.G10,2:B.G13
  step#1  pm(>>,forward)  area=10.34 rise=3.35 twist=31.4
  strand#1  U RNA glyco-bond=-- nts=2 GG 1:B.G9,1:B.G10
  strand#2  U RNA glyco-bond=-- nts=2 GG 1:B.G12,1:B.G13
  strand#3  U RNA glyco-bond=-- nts=2 GG 2:B.G9,2:B.G10
  strand#4  U RNA glyco-bond=-- nts=2 GG 2:B.G12,2:B.G13
  loop#1 type=propeller strands=[#1,#2] nts=1 C 1:B.C11
  loop#2 type=propeller strands=[#3,#4] nts=1 C 2:B.C11

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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]  [3'/5']

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