Detailed DSSR results for the G-quadruplex: PDB entry 2n4y
Created and maintained by Xiang-Jun Lu <xiangjun@x3dna.org>
Citation: Please cite the NAR'20 DSSR-PyMOL schematics paper and/or the NAR'15 DSSR method paper.
Summary information
- 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 CJ, Heddi B, Regmi S, Frasson I, Perrone R, Richter SN, Phan AT (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. doi: 10.1093/nar/gkw432.
- 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
List of 3 G-tetrads
1 glyco-bond=---- sugar=---- groove=---- planarity=0.204 type=other nts=4 GGGG A.DG3,A.DG7,A.DG14,A.DG18 2 glyco-bond=---- sugar=---3 groove=---- planarity=0.292 type=other nts=4 GGGG A.DG4,A.DG8,A.DG15,A.DG20 3 glyco-bond=---- sugar=---- groove=---- planarity=0.479 type=bowl nts=4 GGGG A.DG5,A.DG9,A.DG16,A.DG21
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-tetrad layers, INTRA-molecular, with 1 stem
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG14,A.DG18 2 glyco-bond=---- sugar=---3 groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG15,A.DG20 3 glyco-bond=---- sugar=---- 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=--- sugar=--- nts=3 GGG A.DG3,A.DG4,A.DG5 strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG7,A.DG8,A.DG9 strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG14,A.DG15,A.DG16 strand#4 DNA glyco-bond=--- sugar=-3- nts=3 GGG A.DG18,A.DG20,A.DG21 |
| 2 stacking diagrams | |
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG14,A.DG18 |
 |
2 glyco-bond=---- sugar=---3 groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG15,A.DG20 |
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-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 3(-P-P-P), parallel(4+0)
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG14,A.DG18 2 glyco-bond=---- sugar=---3 groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG15,A.DG20 3 glyco-bond=---- sugar=---- 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=--- sugar=--- nts=3 GGG A.DG3,A.DG4,A.DG5 strand#2 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG7,A.DG8,A.DG9 strand#3 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG14,A.DG15,A.DG16 strand#4* U DNA glyco-bond=--- sugar=-3- 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 |