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

PDB-id
4rkv*
Class
RNA
Method
X-ray (0.88 Å)
Summary
Structural variations and solvent structure of uggggu quadruplexes stabilized by sr2+ ions
Reference
Fyfe, A.C., Dunten, P.W., Martick, M.M., Scott, W.G.: (2015) "Structural Variations and Solvent Structure of r(UGGGGU) Quadruplexes Stabilized by Sr(2+) Ions." J.Mol.Biol., 427, 2205-2219.
Abstract
Guanine-rich sequences can, under appropriate conditions, adopt a distinctive, four-stranded, helical fold known as a G-quadruplex. Interest in quadruplex folds has grown in recent years as evidence of their biological relevance has accumulated from both sequence analysis and function-specific assays. The folds are unusually stable and their formation appears to require close management to maintain cell health; regulatory failure correlates with genomic instability and a number of cancer phenotypes. Biologically relevant quadruplex folds are anticipated to form transiently in mRNA and in single-stranded, unwound DNA. To elucidate factors, including bound solvent, that contribute to the stability of RNA quadruplexes, we examine, by X-ray crystallography and small-angle X-ray scattering, the structure of a previously reported tetramolecular quadruplex, UGGGGU stabilized by Sr(2+) ions. Crystal forms of the octameric assembly formed by this sequence exhibit unusually strong diffraction and anomalous signal enabling the construction of reliable models to a resolution of 0.88Å. The solvent structure confirms hydration patterns reported for other nucleic acid helical conformations and provides support for the greater stability of RNA quadruplexes relative to DNA. Novel features detected in the octameric RNA assembly include a new crystal form, evidence of multiple conformations and structural variations in the 3' U tetrad, including one that leads to the formation of a hydrated internal cavity.
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=0.247 type=other  nts=4 GGGG 1:A.G1002,3:A.G1002,2:A.G1002,4:A.G1002
 2 glyco-bond=---- groove=---- planarity=0.219 type=other  nts=4 GGGG 1:A.G1003,3:A.G1003,2:A.G1003,4:A.G1003
 3 glyco-bond=---- groove=---- planarity=0.133 type=planar nts=4 GGGG 1:A.G1004,3:A.G1004,2:A.G1004,4:A.G1004
 4 glyco-bond=---- groove=---- planarity=0.316 type=bowl   nts=4 GGGG 1:A.G1005,3:A.G1005,2:A.G1005,4:A.G1005
 5 glyco-bond=---- groove=---- planarity=0.268 type=other  nts=4 GGGG 1:B.G2002,4:B.G2002,2:B.G2002,3:B.G2002
 6 glyco-bond=---- groove=---- planarity=0.239 type=bowl   nts=4 GGGG 1:B.G2003,4:B.G2003,2:B.G2003,3:B.G2003
 7 glyco-bond=---- groove=---- planarity=0.109 type=planar nts=4 GGGG 1:B.G2004,4:B.G2004,2:B.G2004,3:B.G2004
 8 glyco-bond=---- groove=---- planarity=0.276 type=bowl   nts=4 GGGG 1:B.G2005,4:B.G2005,2:B.G2005,3:B.G2005

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.G1005,3:A.G1005,2:A.G1005,4:A.G1005
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G1004,3:A.G1004,2:A.G1004,4:A.G1004
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G1003,3:A.G1003,2:A.G1003,4:A.G1003
 4* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G1002,3:A.G1002,2:A.G1002,4:A.G1002
 5  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:B.G2002,4:B.G2002,2:B.G2002,3:B.G2002
 6  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:B.G2003,4:B.G2003,2:B.G2003,3:B.G2003
 7  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:B.G2004,4:B.G2004,2:B.G2004,3:B.G2004
 8  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:B.G2005,4:B.G2005,2:B.G2005,3:B.G2005
  step#1  mp(<<,backward) area=13.10 rise=3.55 twist=24.3
  step#2  mp(<<,backward) area=8.90  rise=3.19 twist=35.0
  step#3  mp(<<,backward) area=12.09 rise=3.47 twist=27.2
  step#4  mm(<>,outward)  area=28.92 rise=3.22 twist=59.7
  step#5  pm(>>,forward)  area=11.49 rise=3.55 twist=27.7
  step#6  pm(>>,forward)  area=9.37  rise=3.18 twist=34.4
  step#7  pm(>>,forward)  area=12.84 rise=3.50 twist=25.4
  strand#1 RNA glyco-bond=-------- nts=8 GGGGGGGG 1:A.G1005,1:A.G1004,1:A.G1003,1:A.G1002,1:B.G2002,1:B.G2003,1:B.G2004,1:B.G2005
  strand#2 RNA glyco-bond=-------- nts=8 GGGGGGGG 3:A.G1005,3:A.G1004,3:A.G1003,3:A.G1002,4:B.G2002,4:B.G2003,4:B.G2004,4:B.G2005
  strand#3 RNA glyco-bond=-------- nts=8 GGGGGGGG 2:A.G1005,2:A.G1004,2:A.G1003,2:A.G1002,2:B.G2002,2:B.G2003,2:B.G2004,2:B.G2005
  strand#4 RNA glyco-bond=-------- nts=8 GGGGGGGG 4:A.G1005,4:A.G1004,4:A.G1003,4:A.G1002,3:B.G2002,3:B.G2003,3:B.G2004,3:B.G2005

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7 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G1005,3:A.G1005,2:A.G1005,4:A.G1005
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G1004,3:A.G1004,2:A.G1004,4:A.G1004
step#1 mp(<<,backward) area=13.10 rise=3.55 twist=24.3

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G1004,3:A.G1004,2:A.G1004,4:A.G1004
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G1003,3:A.G1003,2:A.G1003,4:A.G1003
step#2 mp(<<,backward) area=8.90 rise=3.19 twist=35.0

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 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G1003,3:A.G1003,2:A.G1003,4:A.G1003
4* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G1002,3:A.G1002,2:A.G1002,4:A.G1002
step#3 mp(<<,backward) area=12.09 rise=3.47 twist=27.2

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 4* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G1002,3:A.G1002,2:A.G1002,4:A.G1002
5 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:B.G2002,4:B.G2002,2:B.G2002,3:B.G2002
step#4 mm(<>,outward) area=28.92 rise=3.22 twist=59.7

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 5  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:B.G2002,4:B.G2002,2:B.G2002,3:B.G2002
6 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:B.G2003,4:B.G2003,2:B.G2003,3:B.G2003
step#5 pm(>>,forward) area=11.49 rise=3.55 twist=27.7

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 6  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:B.G2003,4:B.G2003,2:B.G2003,3:B.G2003
7 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:B.G2004,4:B.G2004,2:B.G2004,3:B.G2004
step#6 pm(>>,forward) area=9.37 rise=3.18 twist=34.4

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 7  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:B.G2004,4:B.G2004,2:B.G2004,3:B.G2004
8 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:B.G2005,4:B.G2005,2:B.G2005,3:B.G2005
step#7 pm(>>,forward) area=12.84 rise=3.50 twist=25.4

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G1002,3:A.G1002,2:A.G1002,4:A.G1002
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G1003,3:A.G1003,2:A.G1003,4:A.G1003
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G1004,3:A.G1004,2:A.G1004,4:A.G1004
 4  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:A.G1005,3:A.G1005,2:A.G1005,4:A.G1005
  step#1  pm(>>,forward)  area=12.09 rise=3.47 twist=27.2
  step#2  pm(>>,forward)  area=8.90  rise=3.19 twist=35.0
  step#3  pm(>>,forward)  area=13.10 rise=3.55 twist=24.3
  strand#1  U RNA glyco-bond=---- nts=4 GGGG 1:A.G1002,1:A.G1003,1:A.G1004,1:A.G1005
  strand#2  U RNA glyco-bond=---- nts=4 GGGG 3:A.G1002,3:A.G1003,3:A.G1004,3:A.G1005
  strand#3  U RNA glyco-bond=---- nts=4 GGGG 2:A.G1002,2:A.G1003,2:A.G1004,2:A.G1005
  strand#4  U RNA glyco-bond=---- nts=4 GGGG 4:A.G1002,4:A.G1003,4:A.G1004,4:A.G1005

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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:B.G2002,4:B.G2002,2:B.G2002,3:B.G2002
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:B.G2003,4:B.G2003,2:B.G2003,3:B.G2003
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:B.G2004,4:B.G2004,2:B.G2004,3:B.G2004
 4  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG 1:B.G2005,4:B.G2005,2:B.G2005,3:B.G2005
  step#1  pm(>>,forward)  area=11.49 rise=3.55 twist=27.7
  step#2  pm(>>,forward)  area=9.37  rise=3.18 twist=34.4
  step#3  pm(>>,forward)  area=12.84 rise=3.50 twist=25.4
  strand#1  U RNA glyco-bond=---- nts=4 GGGG 1:B.G2002,1:B.G2003,1:B.G2004,1:B.G2005
  strand#2  U RNA glyco-bond=---- nts=4 GGGG 4:B.G2002,4:B.G2003,4:B.G2004,4:B.G2005
  strand#3  U RNA glyco-bond=---- nts=4 GGGG 2:B.G2002,2:B.G2003,2:B.G2004,2:B.G2005
  strand#4  U RNA glyco-bond=---- nts=4 GGGG 3:B.G2002,3:B.G2003,3:B.G2004,3:B.G2005

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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)