Summary information and primary citation

PDB-id
5mta
Class
DNA
Method
NMR
Summary
G-quadruplex formed within promoters of plasmodium falciparum b var genes
Reference
Juribasic Kulcsar M, Gabelica V, Plavec J (2024): "Solution-State Structure of a Long-Loop G-Quadruplex Formed Within Promoters of Plasmodium falciparum B var Genes." Chemistry, 30, e202401190. doi: 10.1002/chem.202401190.
Abstract
We report the high-resolution NMR solution-state structure of an intramolecular G-quadruplex with a diagonal loop of ten nucleotides. The G-quadruplex is formed by a 34-nt DNA sequence, d[CAG<sub>3</sub>T<sub>2</sub>A<sub>2</sub>G<sub>3</sub>TATA<sub>2</sub>CT<sub>3</sub>AG<sub>4</sub>T<sub>2</sub>AG<sub>3</sub>T<sub>2</sub>], named UpsB-Q-1. This sequence is found within promoters of the var genes of Plasmodium falciparum, which play a key role in malaria pathogenesis and evasion of the immune system. The [3+1]-hybrid G-quadruplex formed under physiologically relevant conditions exhibits a unique equilibrium between two structures, both stabilized by base stacking and non-canonical hydrogen bonding. Unique equilibrium of the two closely related 3D structures originates from a North-South repuckering of deoxyribose moiety of residue T27 in the lateral loop. Besides the 12 guanines involved in three G-quartets, most residues in loop regions are involved in interactions at both G-quartet-loop interfaces.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, UUUD, hybrid2, 3+1, 3(-PD+Lw)

Cartoon-block schematics in six views (download the tarball)

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List of 3 G-tetrads

 1 glyco-bond=sss- sugar=---- groove=--wn planarity=0.402 type=bowl   N- nts=4 GGGG A.DG3,A.DG10,A.DG30,A.DG25
 2 glyco-bond=---s sugar=---- groove=--wn planarity=0.143 type=planar N+ nts=4 GGGG A.DG4,A.DG11,A.DG31,A.DG24
 3 glyco-bond=---s sugar=---- groove=--wn planarity=0.150 type=planar N+ nts=4 GGGG A.DG5,A.DG12,A.DG32,A.DG23

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, 3 G-tetrads, INTRA-molecular, with 1 stem
 1  glyco-bond=sss- sugar=---- groove=--wn Major-->WC N- nts=4 GGGG A.DG3,A.DG10,A.DG30,A.DG25
 2  glyco-bond=---s sugar=---- groove=--wn WC-->Major N+ nts=4 GGGG A.DG4,A.DG11,A.DG31,A.DG24
 3  glyco-bond=---s sugar=---- groove=--wn WC-->Major N+ nts=4 GGGG A.DG5,A.DG12,A.DG32,A.DG23
  step#1  mm(<>,outward)  area=18.13 rise=3.56 twist=14.4
  step#2  pm(>>,forward)  area=13.83 rise=3.34 twist=24.8
  strand#1 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG3,A.DG4,A.DG5
  strand#2 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG10,A.DG11,A.DG12
  strand#3 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG30,A.DG31,A.DG32
  strand#4 DNA glyco-bond=-ss sugar=--- nts=3 GGG A.DG25,A.DG24,A.DG23

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2 stacking diagrams 
 1  glyco-bond=sss- sugar=---- groove=--wn Major-->WC N- nts=4 GGGG A.DG3,A.DG10,A.DG30,A.DG25
 2  glyco-bond=---s sugar=---- groove=--wn WC-->Major N+ nts=4 GGGG A.DG4,A.DG11,A.DG31,A.DG24
  step#1  mm(<>,outward)  area=18.13 rise=3.56 twist=14.4

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 2  glyco-bond=---s sugar=---- groove=--wn WC-->Major N+ nts=4 GGGG A.DG4,A.DG11,A.DG31,A.DG24
 3  glyco-bond=---s sugar=---- groove=--wn WC-->Major N+ nts=4 GGGG A.DG5,A.DG12,A.DG32,A.DG23
  step#2  pm(>>,forward)  area=13.83 rise=3.34 twist=24.8

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List of 1 G4-stem

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-tetrads, 3 loops, INTRA-molecular, UUUD, hybrid2, 3+1, 3(-PD+Lw)
 1  glyco-bond=sss- sugar=---- groove=--wn Major-->WC N- nts=4 GGGG A.DG3,A.DG10,A.DG30,A.DG25
 2  glyco-bond=---s sugar=---- groove=--wn WC-->Major N+ nts=4 GGGG A.DG4,A.DG11,A.DG31,A.DG24
 3  glyco-bond=---s sugar=---- groove=--wn WC-->Major N+ nts=4 GGGG A.DG5,A.DG12,A.DG32,A.DG23
  step#1  mm(<>,outward)  area=18.13 rise=3.56 twist=14.4
  step#2  pm(>>,forward)  area=13.83 rise=3.34 twist=24.8
  strand#1  U DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG3,A.DG4,A.DG5
  strand#2  U DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG10,A.DG11,A.DG12
  strand#3  U DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG30,A.DG31,A.DG32
  strand#4  D DNA glyco-bond=-ss sugar=--- nts=3 GGG A.DG25,A.DG24,A.DG23
  loop#1 type=propeller strands=[#1,#2] nts=4 TTAA A.DT6,A.DT7,A.DA8,A.DA9
  loop#2 type=diagonal  strands=[#2,#4] nts=10 TATAACTTTA A.DT13,A.DA14,A.DT15,A.DA16,A.DA17,A.DC18,A.DT19,A.DT20,A.DT21,A.DA22
  loop#3 type=lateral   strands=[#4,#3] nts=4 GTTA A.DG26,A.DT27,A.DT28,A.DA29

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