Summary information

PDB id
4rj1
Class
RNA
Method
X-ray (0.92 Å)
Summary
Structural variations and solvent structure of uggggu quadruplexes stabilized by sr2+ ions
Reference
Fyfe AC, Dunten PW, Martick MM, Scott WG (2015): "Structural Variations and Solvent Structure of r(UGGGGU) Quadruplexes Stabilized by Sr(2+) Ions." J.Mol.Biol., 427, 2205-2219. doi: 10.1016/j.jmb.2015.03.022.
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

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List of 8 G-tetrads

 1 glyco-bond=---- sugar=3333 groove=---- planarity=0.243 type=other  nts=4 GGGG 1:A.G1002,3:A.G1002,2:A.G1002,4:A.G1002
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.225 type=other  nts=4 GGGG 1:A.G1003,3:A.G1003,2:A.G1003,4:A.G1003
 3 glyco-bond=---- sugar=3333 groove=---- planarity=0.176 type=other  nts=4 GGGG 1:A.G1004,3:A.G1004,2:A.G1004,4:A.G1004
 4 glyco-bond=---- sugar=3333 groove=---- planarity=0.264 type=bowl   nts=4 GGGG 1:A.G1005,3:A.G1005,2:A.G1005,4:A.G1005
 5 glyco-bond=---- sugar=3333 groove=---- planarity=0.281 type=other  nts=4 GGGG 1:B.G2002,4:B.G2002,2:B.G2002,3:B.G2002
 6 glyco-bond=---- sugar=---- groove=---- planarity=0.235 type=bowl   nts=4 GGGG 1:B.G2003,4:B.G2003,2:B.G2003,3:B.G2003
 7 glyco-bond=---- sugar=3333 groove=---- planarity=0.111 type=planar nts=4 GGGG 1:B.G2004,4:B.G2004,2:B.G2004,3:B.G2004
 8 glyco-bond=---- sugar=3333 groove=---- planarity=0.266 type=bowl   nts=4 GGGG 1:B.G2005,4:B.G2005,2:B.G2005,3:B.G2005

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=3333 groove=---- WC-->Major nts=4 GGGG 1:A.G1005,3:A.G1005,2:A.G1005,4:A.G1005
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:A.G1004,3:A.G1004,2:A.G1004,4:A.G1004
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:A.G1003,3:A.G1003,2:A.G1003,4:A.G1003
 4* glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:A.G1002,3:A.G1002,2:A.G1002,4:A.G1002
 5  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:B.G2002,4:B.G2002,2:B.G2002,3:B.G2002
 6  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:B.G2003,4:B.G2003,2:B.G2003,3:B.G2003
 7  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:B.G2004,4:B.G2004,2:B.G2004,3:B.G2004
 8  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:B.G2005,4:B.G2005,2:B.G2005,3:B.G2005
  step#1  mp(<<,backward) area=11.92 rise=3.59 twist=26.0
  step#2  mp(<<,backward) area=9.12  rise=3.17 twist=35.6
  step#3  mp(<<,backward) area=11.82 rise=3.47 twist=27.4
  step#4  mm(<>,outward)  area=29.12 rise=3.19 twist=60.3
  step#5  pm(>>,forward)  area=11.29 rise=3.56 twist=28.0
  step#6  pm(>>,forward)  area=9.13  rise=3.17 twist=34.5
  step#7  pm(>>,forward)  area=13.16 rise=3.48 twist=25.2
  strand#1 RNA glyco-bond=-------- sugar=33-33-33 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=-------- sugar=33-33-33 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=-------- sugar=33-33-33 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=-------- sugar=33-33-33 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=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:A.G1005,3:A.G1005,2:A.G1005,4:A.G1005
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:A.G1004,3:A.G1004,2:A.G1004,4:A.G1004
  step#1  mp(<<,backward) area=11.92 rise=3.59 twist=26.0

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 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:A.G1004,3:A.G1004,2:A.G1004,4:A.G1004
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:A.G1003,3:A.G1003,2:A.G1003,4:A.G1003
  step#2  mp(<<,backward) area=9.12  rise=3.17 twist=35.6

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 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:A.G1003,3:A.G1003,2:A.G1003,4:A.G1003
 4* glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:A.G1002,3:A.G1002,2:A.G1002,4:A.G1002
  step#3  mp(<<,backward) area=11.82 rise=3.47 twist=27.4

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 4* glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:A.G1002,3:A.G1002,2:A.G1002,4:A.G1002
 5  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:B.G2002,4:B.G2002,2:B.G2002,3:B.G2002
  step#4  mm(<>,outward)  area=29.12 rise=3.19 twist=60.3

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 5  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:B.G2002,4:B.G2002,2:B.G2002,3:B.G2002
 6  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:B.G2003,4:B.G2003,2:B.G2003,3:B.G2003
  step#5  pm(>>,forward)  area=11.29 rise=3.56 twist=28.0

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 6  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:B.G2003,4:B.G2003,2:B.G2003,3:B.G2003
 7  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:B.G2004,4:B.G2004,2:B.G2004,3:B.G2004
  step#6  pm(>>,forward)  area=9.13  rise=3.17 twist=34.5

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 7  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:B.G2004,4:B.G2004,2:B.G2004,3:B.G2004
 8  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:B.G2005,4:B.G2005,2:B.G2005,3:B.G2005
  step#7  pm(>>,forward)  area=13.16 rise=3.48 twist=25.2

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

 1  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:A.G1002,3:A.G1002,2:A.G1002,4:A.G1002
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:A.G1003,3:A.G1003,2:A.G1003,4:A.G1003
 3  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:A.G1004,3:A.G1004,2:A.G1004,4:A.G1004
 4  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:A.G1005,3:A.G1005,2:A.G1005,4:A.G1005
  step#1  pm(>>,forward)  area=11.82 rise=3.47 twist=27.4
  step#2  pm(>>,forward)  area=9.12  rise=3.17 twist=35.6
  step#3  pm(>>,forward)  area=11.92 rise=3.59 twist=26.0
  strand#1  U RNA glyco-bond=---- sugar=3-33 nts=4 GGGG 1:A.G1002,1:A.G1003,1:A.G1004,1:A.G1005
  strand#2  U RNA glyco-bond=---- sugar=3-33 nts=4 GGGG 3:A.G1002,3:A.G1003,3:A.G1004,3:A.G1005
  strand#3  U RNA glyco-bond=---- sugar=3-33 nts=4 GGGG 2:A.G1002,2:A.G1003,2:A.G1004,2:A.G1005
  strand#4  U RNA glyco-bond=---- sugar=3-33 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=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:B.G2002,4:B.G2002,2:B.G2002,3:B.G2002
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:B.G2003,4:B.G2003,2:B.G2003,3:B.G2003
 3  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:B.G2004,4:B.G2004,2:B.G2004,3:B.G2004
 4  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG 1:B.G2005,4:B.G2005,2:B.G2005,3:B.G2005
  step#1  pm(>>,forward)  area=11.29 rise=3.56 twist=28.0
  step#2  pm(>>,forward)  area=9.13  rise=3.17 twist=34.5
  step#3  pm(>>,forward)  area=13.16 rise=3.48 twist=25.2
  strand#1  U RNA glyco-bond=---- sugar=3-33 nts=4 GGGG 1:B.G2002,1:B.G2003,1:B.G2004,1:B.G2005
  strand#2  U RNA glyco-bond=---- sugar=3-33 nts=4 GGGG 4:B.G2002,4:B.G2003,4:B.G2004,4:B.G2005
  strand#3  U RNA glyco-bond=---- sugar=3-33 nts=4 GGGG 2:B.G2002,2:B.G2003,2:B.G2004,2:B.G2005
  strand#4  U RNA glyco-bond=---- sugar=3-33 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

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