Detailed DSSR results for the G-quadruplex: PDB entry 8f0n
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
- 8f0n
- Class
- RNA
- Method
- X-ray (2.85 Å)
- Summary
- Wobble beetroot (a16u-u38g) dimer bound to dfho
- Reference
- Passalacqua LFM, Starich MR, Link KA, Wu J, Knutson JR, Tjandra N, Jaffrey SR, Ferre-D'Amare AR (2023): "Co-crystal structures of the fluorogenic aptamer Beetroot show that close homology may not predict similar RNA architecture." Nat Commun, 14, 2969. doi: 10.1038/s41467-023-38683-3.
- Abstract
- Beetroot is a homodimeric in vitro selected RNA that binds and activates DFAME, a conditional fluorophore derived from GFP. It is 70% sequence-identical to the previously characterized homodimeric aptamer Corn, which binds one molecule of its cognate fluorophore DFHO at its interprotomer interface. We have now determined the Beetroot-DFAME co-crystal structure at 1.95 Å resolution, discovering that this RNA homodimer binds two molecules of the fluorophore, at sites separated by ~30 Å. In addition to this overall architectural difference, the local structures of the non-canonical, complex quadruplex cores of Beetroot and Corn are distinctly different, underscoring how subtle RNA sequence differences can give rise to unexpected structural divergence. Through structure-guided engineering, we generated a variant that has a 12-fold fluorescence activation selectivity switch toward DFHO. Beetroot and this variant form heterodimers and constitute the starting point for engineered tags whose through-space inter-fluorophore interaction could be used to monitor RNA dimerization.
- G4 notes
- 6 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack, 2(-P-P-P), parallel(4+0), UUUU, coaxial interfaces: 5'/5'
Base-block schematics in six views
List of 6 G-tetrads
1 glyco-bond=ss-- sugar=---- groove=-w-n planarity=0.325 type=bowl nts=4 GGGG B.G18,B.G35,B.G27,B.G22 2 glyco-bond=---- sugar=-333 groove=---- planarity=0.306 type=other nts=4 GGGG B.G20,B.G24,B.G29,B.G32 3 glyco-bond=---- sugar=33-3 groove=---- planarity=0.181 type=other nts=4 GGGG B.G21,B.G25,B.G30,B.G33 4 glyco-bond=ss-- sugar=---- groove=-w-n planarity=0.389 type=other nts=4 GGGG A.G18,A.G35,A.G27,A.G22 5 glyco-bond=---- sugar=-333 groove=---- planarity=0.341 type=other nts=4 GGGG A.G20,A.G24,A.G29,A.G32 6 glyco-bond=---- sugar=33-3 groove=---- planarity=0.195 type=other nts=4 GGGG A.G21,A.G25,A.G30,A.G33
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, 6 G-tetrad layers, inter-molecular, with 2 stems
 |
1 glyco-bond=ss-- sugar=---- groove=-w-n Major-->WC nts=4 GGGG B.G18,B.G35,B.G27,B.G22 2 glyco-bond=---- sugar=3-33 groove=---- Major-->WC nts=4 GGGG B.G33,B.G30,B.G25,B.G21 3* glyco-bond=---- sugar=333- groove=---- Major-->WC nts=4 GGGG B.G32,B.G29,B.G24,B.G20 4 glyco-bond=---- sugar=3-33 groove=---- WC-->Major nts=4 GGGG A.G32,A.G20,A.G24,A.G29 5 glyco-bond=---- sugar=333- groove=---- WC-->Major nts=4 GGGG A.G33,A.G21,A.G25,A.G30 6 glyco-bond=s--s sugar=---- groove=n-w- WC-->Major nts=4 GGGG A.G18,A.G22,A.G27,A.G35 step#1 mp(<<,backward) area=8.36 rise=3.52 twist=33.4 step#2 mp(<<,backward) area=8.50 rise=3.41 twist=30.9 step#3 mm(<>,outward) area=7.33 rise=3.26 twist=-57.4 step#4 pm(>>,forward) area=10.25 rise=3.45 twist=30.4 step#5 pm(>>,forward) area=6.44 rise=3.51 twist=35.3 strand#1 RNA glyco-bond=s----s sugar=-3333- nts=6 GGGGGG B.G18,B.G33,B.G32,A.G32,A.G33,A.G18 strand#2 RNA glyco-bond=s----- sugar=--3-3- nts=6 GGGGGG B.G35,B.G30,B.G29,A.G20,A.G21,A.G22 strand#3 RNA glyco-bond=------ sugar=-3333- nts=6 GGGGGG B.G27,B.G25,B.G24,A.G24,A.G25,A.G27 strand#4 RNA glyco-bond=-----s sugar=-3-3-- nts=6 GGGGGG B.G22,B.G21,B.G20,A.G29,A.G30,A.G35 |
| 5 stacking diagrams | |
 |
1 glyco-bond=ss-- sugar=---- groove=-w-n Major-->WC nts=4 GGGG B.G18,B.G35,B.G27,B.G22 |
 |
2 glyco-bond=---- sugar=3-33 groove=---- Major-->WC nts=4 GGGG B.G33,B.G30,B.G25,B.G21 |
 |
3* glyco-bond=---- sugar=333- groove=---- Major-->WC nts=4 GGGG B.G32,B.G29,B.G24,B.G20 |
 |
4 glyco-bond=---- sugar=3-33 groove=---- WC-->Major nts=4 GGGG A.G32,A.G20,A.G24,A.G29 |
 |
5 glyco-bond=---- sugar=333- groove=---- WC-->Major nts=4 GGGG A.G33,A.G21,A.G25,A.G30 |
List of 2 G4-stems
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, UUUU, parallel, 2(-P-P-P), parallel(4+0)
 |
1 glyco-bond=---- sugar=-333 groove=---- WC-->Major nts=4 GGGG B.G20,B.G24,B.G29,B.G32 2 glyco-bond=---- sugar=33-3 groove=---- WC-->Major nts=4 GGGG B.G21,B.G25,B.G30,B.G33 step#1 pm(>>,forward) area=8.50 rise=3.41 twist=30.9 strand#1 U RNA glyco-bond=-- sugar=-3 nts=2 GG B.G20,B.G21 strand#2 U RNA glyco-bond=-- sugar=33 nts=2 GG B.G24,B.G25 strand#3 U RNA glyco-bond=-- sugar=3- nts=2 GG B.G29,B.G30 strand#4 U RNA glyco-bond=-- sugar=33 nts=2 GG B.G32,B.G33 loop#1 type=propeller strands=[#1,#2] nts=2 GU B.G22,B.U23 loop#2 type=propeller strands=[#2,#3] nts=3 UGU B.U26,B.G27,B.U28 loop#3 type=propeller strands=[#3,#4] nts=1 A B.A31 |
Stem#2, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)
 |
1 glyco-bond=---- sugar=-333 groove=---- WC-->Major nts=4 GGGG A.G20,A.G24,A.G29,A.G32 2 glyco-bond=---- sugar=33-3 groove=---- WC-->Major nts=4 GGGG A.G21,A.G25,A.G30,A.G33 step#1 pm(>>,forward) area=10.25 rise=3.45 twist=30.4 strand#1 U RNA glyco-bond=-- sugar=-3 nts=2 GG A.G20,A.G21 strand#2 U RNA glyco-bond=-- sugar=33 nts=2 GG A.G24,A.G25 strand#3 U RNA glyco-bond=-- sugar=3- nts=2 GG A.G29,A.G30 strand#4 U RNA glyco-bond=-- sugar=33 nts=2 GG A.G32,A.G33 loop#1 type=propeller strands=[#1,#2] nts=2 GU A.G22,A.U23 loop#2 type=propeller strands=[#2,#3] nts=3 UGU A.U26,A.G27,A.U28 loop#3 type=propeller strands=[#3,#4] nts=1 A A.A31 |
List of 1 G4 coaxial stack
1 G4 helix#1 contains 2 G4 stems: [#1,#2] [5'/5']