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

PDB-id
5o4d
Class
DNA
Method
NMR
Summary
G-quadruplex of human papillomavirus type 52
Reference
Marusic, M., Plavec, J.: (2019) "Towards Understanding of Polymorphism of the G-rich Region of Human Papillomavirus Type 52." Molecules, 24
Abstract
The potential to affect gene expression via G-quadruplex stabilization has been extended to all domains of life, including viruses. Here, we investigate the polymorphism and structures of G-quadruplexes of the human papillomavirus type 52 with UV, CD and NMR spectroscopy and gel electrophoresis. We show that oligonucleotide with five G-tracts folds into several structures and that naturally occurring single nucleotide polymorphisms (SNPs) have profound effects on the structural polymorphism in the context of G-quadruplex forming propensity, conformational heterogeneity and folding stability. With help of SNP analysis, we were able to select one of the predominant forms, formed by G-rich sequence d(G₃TAG₃CAG₄ACACAG₃T). This oligonucleotide termed HPV52(1-4) adopts a three G-quartet snap back (3 + 1) type scaffold with four syn guanine residues, two edgewise loops spanning the same groove, a no-residue V loop and a propeller type loop. The first guanine residue is incorporated in the central G-quartet and all four-guanine residues from G4 stretch are included in the three quartet G-quadruplex core. Modification studies identified several structural elements that are important for stabilization of the described G-quadruplex fold. Our results expand set of G-rich targets in viral genomes and address the fundamental questions regarding folding of G-rich sequences.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · 2(-LwX+P), UD3(1+3), UDDD

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

PyMOL session file PDB file View in 3Dmol.js

List of 3 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=s--- groove=w--n planarity=0.324 type=other  nts=4 GGGG A.DG1,A.DG7,A.DG21,A.DG13
 2 glyco-bond=-ss- groove=w-n- planarity=0.525 type=bowl   nts=4 GGGG A.DG2,A.DG6,A.DG20,A.DG12
 3 glyco-bond=-s-- groove=wn-- planarity=0.398 type=other  nts=4 GGGG A.DG8,A.DG11,A.DG14,A.DG22

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, 3 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG20,A.DG12
 2  glyco-bond=s--- groove=w--n Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG21,A.DG13
 3  glyco-bond=s--- groove=w--n Major-->WC nts=4 GGGG A.DG11,A.DG8,A.DG22,A.DG14
  step#1  mm(<>,outward)  area=10.18 rise=3.57 twist=24.1
  step#2  pm(>>,forward)  area=14.46 rise=3.43 twist=25.9
  strand#1 DNA glyco-bond=-ss nts=3 GGG A.DG2,A.DG1,A.DG11
  strand#2 DNA glyco-bond=s-- nts=3 GGG A.DG6,A.DG7,A.DG8
  strand#3 DNA glyco-bond=s-- nts=3 GGG A.DG20,A.DG21,A.DG22
  strand#4 DNA glyco-bond=--- nts=3 GGG A.DG12,A.DG13,A.DG14

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2 stacking diagrams
 1  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG20,A.DG12
2 glyco-bond=s--- groove=w--n Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG21,A.DG13
step#1 mm(<>,outward) area=10.18 rise=3.57 twist=24.1

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 2  glyco-bond=s--- groove=w--n Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG21,A.DG13
3 glyco-bond=s--- groove=w--n Major-->WC nts=4 GGGG A.DG11,A.DG8,A.DG22,A.DG14
step#2 pm(>>,forward) area=14.46 rise=3.43 twist=25.9

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List of 1 G4-stem [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, 3 loops, INTRA-molecular, UDDD, anti-parallel, 2(-LwX+P), UD3(1+3)

 1  glyco-bond=s--- groove=w--n Major-->WC nts=4 GGGG A.DG1,A.DG7,A.DG21,A.DG13
 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,A.DG6,A.DG20,A.DG12
  step#1  mm(<>,outward)  area=10.18 rise=3.57 twist=24.1
  strand#1  U DNA glyco-bond=s- nts=2 GG A.DG1,A.DG2
  strand#2  D DNA glyco-bond=-s nts=2 GG A.DG7,A.DG6
  strand#3  D DNA glyco-bond=-s nts=2 GG A.DG21,A.DG20
  strand#4  D DNA glyco-bond=-- nts=2 GG A.DG13,A.DG12
  loop#1 type=lateral   strands=[#1,#2] nts=3 GTA A.DG3,A.DT4,A.DA5
  loop#2 type=diag-prop strands=[#2,#4] nts=4 GCAG A.DG8,A.DC9,A.DA10,A.DG11
  loop#3 type=propeller strands=[#4,#3] nts=6 GACACA A.DG14,A.DA15,A.DC16,A.DA17,A.DC18,A.DA19

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List of 0 G4 coaxial stacks [summary · schematics · tetrads · helices · stems · homepage]

List of 2 non-stem G4-loops (including the two closing Gs)

 1 type=lateral   helix=#1 nts=4 GCAG A.DG8,A.DC9,A.DA10,A.DG11
 2 type=V-shaped  helix=#1 nts=4 GGGG A.DG11,A.DG12,A.DG13,A.DG14