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

PDB-id
2lxv
Class
DNA
Method
NMR
Summary
Dimeric pil-e G-quadruplex DNA from neisseria gonorrhoeae, NMR 11 structures
Reference
Kuryavyi, V., Cahoon, L.A., Seifert, H.S., Patel, D.J.: (2012) "RecA-Binding pilE G4 Sequence Essential for Pilin Antigenic Variation Forms Monomeric and 5' End-Stacked Dimeric Parallel G-Quadruplexes." Structure, 20, 2090-2102.
Abstract
Neisseria gonorrhoeae is an obligate human pathogen that can escape immune surveillance through antigenic variation of surface structures such as pili. A G-quadruplex-forming (G4) sequence (5'-G(3)TG(3)TTG(3)TG(3)) located upstream of the N. gonorrhoeae pilin expression locus (pilE) is necessary for initiation of pilin antigenic variation, a recombination-based, high-frequency, diversity-generation system. We have determined NMR-based structures of the all parallel-stranded monomeric and 5' end-stacked dimeric pilE G-quadruplexes in monovalent cation-containing solutions. We demonstrate that the three-layered all parallel-stranded monomeric pilE G-quadruplex containing single-residue double-chain reversal loops, which can be modeled without steric clashes into the 3 nt DNA-binding site of RecA, binds and promotes E. coli RecA-mediated strand exchange in vitro. We discuss how interactions between RecA and monomeric pilE G-quadruplex could facilitate the specialized recombination reactions leading to pilin diversification.
G4 notes
6 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack · 3(-P-P-P), parallel(4+0), UUUU · coaxial interfaces: 5'/5'

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

PyMOL session file PDB file View in 3Dmol.js

List of 6 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=---- groove=---- planarity=0.129 type=planar nts=4 GGGG A.DG1,A.DG5,A.DG10,A.DG14
 2 glyco-bond=---- groove=---- planarity=0.064 type=planar nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG15
 3 glyco-bond=---- groove=---- planarity=0.165 type=other  nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG16
 4 glyco-bond=---- groove=---- planarity=0.130 type=planar nts=4 GGGG B.DG1,B.DG5,B.DG10,B.DG14
 5 glyco-bond=---- groove=---- planarity=0.064 type=planar nts=4 GGGG B.DG2,B.DG6,B.DG11,B.DG15
 6 glyco-bond=---- groove=---- planarity=0.165 type=other  nts=4 GGGG B.DG3,B.DG7,B.DG12,B.DG16

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.DG3,A.DG7,A.DG12,A.DG16
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG15
 3* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG5,A.DG10,A.DG14
 4  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG5,B.DG1,B.DG14,B.DG10
 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG6,B.DG2,B.DG15,B.DG11
 6  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG7,B.DG3,B.DG16,B.DG12
  step#1  mp(<<,backward) area=14.69 rise=3.43 twist=25.8
  step#2  mp(<<,backward) area=12.83 rise=3.38 twist=28.6
  step#3  mm(<>,outward)  area=27.74 rise=3.17 twist=-27.1
  step#4  pm(>>,forward)  area=12.84 rise=3.38 twist=28.5
  step#5  pm(>>,forward)  area=14.69 rise=3.43 twist=25.8
  strand#1 DNA glyco-bond=------ nts=6 GGGGGG A.DG3,A.DG2,A.DG1,B.DG5,B.DG6,B.DG7
  strand#2 DNA glyco-bond=------ nts=6 GGGGGG A.DG7,A.DG6,A.DG5,B.DG1,B.DG2,B.DG3
  strand#3 DNA glyco-bond=------ nts=6 GGGGGG A.DG12,A.DG11,A.DG10,B.DG14,B.DG15,B.DG16
  strand#4 DNA glyco-bond=------ nts=6 GGGGGG A.DG16,A.DG15,A.DG14,B.DG10,B.DG11,B.DG12

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5 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG16
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG15
step#1 mp(<<,backward) area=14.69 rise=3.43 twist=25.8

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG15
3* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG5,A.DG10,A.DG14
step#2 mp(<<,backward) area=12.83 rise=3.38 twist=28.6

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 3* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG5,A.DG10,A.DG14
4 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG5,B.DG1,B.DG14,B.DG10
step#3 mm(<>,outward) area=27.74 rise=3.17 twist=-27.1

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 4  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG5,B.DG1,B.DG14,B.DG10
5 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG6,B.DG2,B.DG15,B.DG11
step#4 pm(>>,forward) area=12.84 rise=3.38 twist=28.5

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 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG6,B.DG2,B.DG15,B.DG11
6 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG7,B.DG3,B.DG16,B.DG12
step#5 pm(>>,forward) area=14.69 rise=3.43 twist=25.8

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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, 3 loops, INTRA-molecular, UUUU, parallel, 3(-P-P-P), parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG1,A.DG5,A.DG10,A.DG14
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG11,A.DG15
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG16
  step#1  pm(>>,forward)  area=12.83 rise=3.38 twist=28.6
  step#2  pm(>>,forward)  area=14.69 rise=3.43 twist=25.8
  strand#1  U DNA glyco-bond=--- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2  U DNA glyco-bond=--- nts=3 GGG A.DG5,A.DG6,A.DG7
  strand#3  U DNA glyco-bond=--- nts=3 GGG A.DG10,A.DG11,A.DG12
  strand#4  U DNA glyco-bond=--- nts=3 GGG A.DG14,A.DG15,A.DG16
  loop#1 type=propeller strands=[#1,#2] nts=1 T A.DT4
  loop#2 type=propeller strands=[#2,#3] nts=2 TT A.DT8,A.DT9
  loop#3 type=propeller strands=[#3,#4] nts=1 T A.DT13

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG1,B.DG5,B.DG10,B.DG14
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG2,B.DG6,B.DG11,B.DG15
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG7,B.DG12,B.DG16
  step#1  pm(>>,forward)  area=12.84 rise=3.38 twist=28.5
  step#2  pm(>>,forward)  area=14.69 rise=3.43 twist=25.8
  strand#1  U DNA glyco-bond=--- nts=3 GGG B.DG1,B.DG2,B.DG3
  strand#2  U DNA glyco-bond=--- nts=3 GGG B.DG5,B.DG6,B.DG7
  strand#3  U DNA glyco-bond=--- nts=3 GGG B.DG10,B.DG11,B.DG12
  strand#4  U DNA glyco-bond=--- nts=3 GGG B.DG14,B.DG15,B.DG16
  loop#1 type=propeller strands=[#1,#2] nts=1 T B.DT4
  loop#2 type=propeller strands=[#2,#3] nts=2 TT B.DT8,B.DT9
  loop#3 type=propeller strands=[#3,#4] nts=1 T B.DT13

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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)