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

PDB-id
2n4y
Class
DNA
Method
NMR
Summary
Structure and possible function of a G-quadruplex in the long terminal repeat of the proviral hiv-1 genome
Reference
De Nicola, B., Lech, C.J., Heddi, B., Regmi, S., Frasson, I., Perrone, R., Richter, S.N., Phan, A.T.: (2016) "Structure and possible function of a G-quadruplex in the long terminal repeat of the proviral HIV-1 genome." Nucleic Acids Res., 44, 6442-6451.
Abstract
The long terminal repeat (LTR) of the proviral human immunodeficiency virus (HIV)-1 genome is integral to virus transcription and host cell infection. The guanine-rich U3 region within the LTR promoter, previously shown to form G-quadruplex structures, represents an attractive target to inhibit HIV transcription and replication. In this work, we report the structure of a biologically relevant G-quadruplex within the LTR promoter region of HIV-1. The guanine-rich sequence designated LTR-IV forms a well-defined structure in physiological cationic solution. The nuclear magnetic resonance (NMR) structure of this sequence reveals a parallel-stranded G-quadruplex containing a single-nucleotide thymine bulge, which participates in a conserved stacking interaction with a neighboring single-nucleotide adenine loop. Transcription analysis in a HIV-1 replication competent cell indicates that the LTR-IV region may act as a modulator of G-quadruplex formation in the LTR promoter. Consequently, the LTR-IV G-quadruplex structure presented within this work could represent a valuable target for the design of HIV therapeutics.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · 3(-P-P-P), parallel(4+0), UUUU

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=---- groove=---- planarity=0.204 type=other  nts=4 GGGG A.DG3,A.DG7,A.DG14,A.DG18
 2 glyco-bond=---- groove=---- planarity=0.292 type=other  nts=4 GGGG A.DG4,A.DG8,A.DG15,A.DG20
 3 glyco-bond=---- groove=---- planarity=0.479 type=bowl   nts=4 GGGG A.DG5,A.DG9,A.DG16,A.DG21

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=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG14,A.DG18
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG15,A.DG20
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG16,A.DG21
  step#1  pm(>>,forward)  area=12.91 rise=3.31 twist=28.0
  step#2  pm(>>,forward)  area=10.80 rise=3.47 twist=28.0
  strand#1 DNA glyco-bond=--- nts=3 GGG A.DG3,A.DG4,A.DG5
  strand#2 DNA glyco-bond=--- nts=3 GGG A.DG7,A.DG8,A.DG9
  strand#3 DNA glyco-bond=--- nts=3 GGG A.DG14,A.DG15,A.DG16
  strand#4 DNA glyco-bond=--- nts=3 GGG A.DG18,A.DG20,A.DG21

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2 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG14,A.DG18
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG15,A.DG20
step#1 pm(>>,forward) area=12.91 rise=3.31 twist=28.0

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG15,A.DG20
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG16,A.DG21
step#2 pm(>>,forward) area=10.80 rise=3.47 twist=28.0

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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, 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.DG3,A.DG7,A.DG14,A.DG18
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG15,A.DG20
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG16,A.DG21
  step#1  pm(>>,forward)  area=12.91 rise=3.31 twist=28.0
  step#2  pm(>>,forward)  area=10.80 rise=3.47 twist=28.0
  strand#1  U DNA glyco-bond=--- nts=3 GGG A.DG3,A.DG4,A.DG5
  strand#2  U DNA glyco-bond=--- nts=3 GGG A.DG7,A.DG8,A.DG9
  strand#3  U DNA glyco-bond=--- nts=3 GGG A.DG14,A.DG15,A.DG16
  strand#4* U DNA glyco-bond=--- nts=3 GGG A.DG18,A.DG20,A.DG21 bulged-nts=1 T A.DT19
  loop#1 type=propeller strands=[#1,#2] nts=1 C A.DC6
  loop#2 type=propeller strands=[#2,#3] nts=4 ACTG A.DA10,A.DC11,A.DT12,A.DG13
  loop#3 type=propeller strands=[#3,#4] nts=1 A A.DA17

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

List of 0 non-stem G4-loops (including the two closing Gs)