DSSR-enabled G4 identification/annotation: PDB entry 8utg
Summary information and primary citation
- PDB-id
- 8utg
- Class
- RNA
- Method
- X-ray (1.97 Å)
- Summary
- An RNA g-quadruplex from the ns5 gene in the west nile virus genome
- Reference
- Terrell JR, Le TT, Paul A, Brinton MA, Wilson WD, Poon GMK, Germann MW, Siemer JL (2024): "Structure of an RNA G-quadruplex from the West Nile virus genome." Nat Commun, 15, 5428. doi: 10.1038/s41467-024-49761-5.
- Abstract
- Potential G-quadruplex sites have been identified in the genomes of DNA and RNA viruses and proposed as regulatory elements. The genus Orthoflavivirus contains arthropod-transmitted, positive-sense, single-stranded RNA viruses that cause significant human disease globally. Computational studies have identified multiple potential G-quadruplex sites that are conserved across members of this genus. Subsequent biophysical studies established that some G-quadruplexes predicted in Zika and tickborne encephalitis virus genomes can form and known quadruplex binders reduced viral yields from cells infected with these viruses. The susceptibility of RNA to degradation and the variability of loop regions have made structure determination challenging. Despite these difficulties, we report a high-resolution structure of the NS5-B quadruplex from the West Nile virus genome. Analysis reveals two stacked tetrads that are further stabilized by a stacked triad and transient noncanonical base pairing. This structure expands the landscape of solved RNA quadruplex structures and demonstrates the diversity and complexity of biological quadruplexes. We anticipate that the availability of this structure will assist in solving further viral RNA quadruplexes and provides a model for a conserved antiviral target in Orthoflavivirus genomes.
- G4 notes
- 2 G-tetrads, 1 G4 helix, 1 G4 stem, UUUU, parallel, 4+0, 2(-P-P-P)
Cartoon-block schematics in six views (download the tarball)
List of 2 G-tetrads
1 glyco-bond=---- sugar=--33 groove=---- planarity=0.136 type=planar O+ nts=4 GGGG 1:A.G4,1:A.G10,1:A.G13,1:A.G17 2 glyco-bond=---- sugar=3-33 groove=---- planarity=0.168 type=other O+ nts=4 GGGG 1:A.G5,1:A.G11,1:A.G14,1:A.G18
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, 2 G-tetrads, INTRA-molecular, with 1 stem
|
1 glyco-bond=---- sugar=--33 groove=---- WC-->Major O+ nts=4 GGGG 1:A.G4,1:A.G10,1:A.G13,1:A.G17 2 glyco-bond=---- sugar=3-33 groove=---- WC-->Major O+ nts=4 GGGG 1:A.G5,1:A.G11,1:A.G14,1:A.G18 step#1 pm(>>,forward) area=7.56 rise=3.35 twist=33.9 strand#1 RNA glyco-bond=-- sugar=-3 nts=2 GG 1:A.G4,1:A.G5 strand#2 RNA glyco-bond=-- sugar=-- nts=2 GG 1:A.G10,1:A.G11 strand#3 RNA glyco-bond=-- sugar=33 nts=2 GG 1:A.G13,1:A.G14 strand#4 RNA glyco-bond=-- sugar=33 nts=2 GG 1:A.G17,1:A.G18 |
| 1 stacking diagram | |
|
1 glyco-bond=---- sugar=--33 groove=---- WC-->Major O+ nts=4 GGGG 1:A.G4,1:A.G10,1:A.G13,1:A.G17 |
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, 2 G-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, 4+0, 2(-P-P-P)
|
1 glyco-bond=---- sugar=--33 groove=---- WC-->Major O+ nts=4 GGGG 1:A.G4,1:A.G10,1:A.G13,1:A.G17 2 glyco-bond=---- sugar=3-33 groove=---- WC-->Major O+ nts=4 GGGG 1:A.G5,1:A.G11,1:A.G14,1:A.G18 step#1 pm(>>,forward) area=7.56 rise=3.35 twist=33.9 strand#1 U RNA glyco-bond=-- sugar=-3 nts=2 GG 1:A.G4,1:A.G5 strand#2 U RNA glyco-bond=-- sugar=-- nts=2 GG 1:A.G10,1:A.G11 strand#3 U RNA glyco-bond=-- sugar=33 nts=2 GG 1:A.G13,1:A.G14 strand#4 U RNA glyco-bond=-- sugar=33 nts=2 GG 1:A.G17,1:A.G18 loop#1 type=propeller strands=[#1,#2] nts=4 AAGA 1:A.A6,1:A.A7,1:A.G8,1:A.A9 loop#2 type=propeller strands=[#2,#3] nts=1 C 1:A.C12 loop#3 type=propeller strands=[#3,#4] nts=2 UU 1:A.U15,1:A.U16 |