DSSR-curated G4 structure: PDB entry 8eyv

Summary information

PDB id: 8eyv
Class: RNA
Method: X-ray (2.55 Å)
Summary: Structure of beetroot 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

PyMOL session file	PDB file	View in 3Dmol.js

List of 6 G-tetrads

 1 glyco-bond=ss-- sugar=---- groove=-w-n planarity=0.348 type=bowl-2 nts=4 GGGG A.G18,A.G35,A.G27,A.G22
 2 glyco-bond=---- sugar=-333 groove=---- planarity=0.298 type=other  nts=4 GGGG A.G20,A.G24,A.G29,A.G32
 3 glyco-bond=---- sugar=33-3 groove=---- planarity=0.189 type=other  nts=4 GGGG A.G21,A.G25,A.G30,A.G33
 4 glyco-bond=ss-- sugar=---- groove=-w-n planarity=0.286 type=bowl   nts=4 GGGG B.G18,B.G35,B.G27,B.G22
 5 glyco-bond=---- sugar=--33 groove=---- planarity=0.220 type=other  nts=4 GGGG B.G20,B.G24,B.G29,B.G32
 6 glyco-bond=---- sugar=33-3 groove=---- planarity=0.170 type=other  nts=4 GGGG B.G21,B.G25,B.G30,B.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 A.G18,A.G35,A.G27,A.G22 2 glyco-bond=---- sugar=3-33 groove=---- Major-->WC nts=4 GGGG A.G33,A.G30,A.G25,A.G21 3* glyco-bond=---- sugar=333- groove=---- Major-->WC nts=4 GGGG A.G32,A.G29,A.G24,A.G20 4 glyco-bond=---- sugar=3--3 groove=---- WC-->Major nts=4 GGGG B.G32,B.G20,B.G24,B.G29 5 glyco-bond=---- sugar=333- groove=---- WC-->Major nts=4 GGGG B.G33,B.G21,B.G25,B.G30 6 glyco-bond=s--s sugar=---- groove=n-w- WC-->Major nts=4 GGGG B.G18,B.G22,B.G27,B.G35 step#1 mp(<<,backward) area=7.94 rise=3.52 twist=32.8 step#2 mp(<<,backward) area=10.71 rise=3.45 twist=30.1 step#3 mm(<>,outward) area=7.82 rise=3.34 twist=-56.4 step#4 pm(>>,forward) area=10.47 rise=3.35 twist=30.0 step#5 pm(>>,forward) area=8.08 rise=3.50 twist=34.1 strand#1 RNA glyco-bond=s----s sugar=-3333- nts=6 GGGGGG A.G18,A.G33,A.G32,B.G32,B.G33,B.G18 strand#2 RNA glyco-bond=s----- sugar=--3-3- nts=6 GGGGGG A.G35,A.G30,A.G29,B.G20,B.G21,B.G22 strand#3 RNA glyco-bond=------ sugar=-33-3- nts=6 GGGGGG A.G27,A.G25,A.G24,B.G24,B.G25,B.G27 strand#4 RNA glyco-bond=-----s sugar=-3-3-- nts=6 GGGGGG A.G22,A.G21,A.G20,B.G29,B.G30,B.G35 Download PDB file Interactive view in 3Dmol.js
5 stacking diagrams
	1 glyco-bond=ss-- sugar=---- groove=-w-n Major-->WC nts=4 GGGG A.G18,A.G35,A.G27,A.G22 2 glyco-bond=---- sugar=3-33 groove=---- Major-->WC nts=4 GGGG A.G33,A.G30,A.G25,A.G21 step#1 mp(<<,backward) area=7.94 rise=3.52 twist=32.8 Download PDB file Interactive view in 3Dmol.js
	2 glyco-bond=---- sugar=3-33 groove=---- Major-->WC nts=4 GGGG A.G33,A.G30,A.G25,A.G21 3* glyco-bond=---- sugar=333- groove=---- Major-->WC nts=4 GGGG A.G32,A.G29,A.G24,A.G20 step#2 mp(<<,backward) area=10.71 rise=3.45 twist=30.1 Download PDB file Interactive view in 3Dmol.js
	3* glyco-bond=---- sugar=333- groove=---- Major-->WC nts=4 GGGG A.G32,A.G29,A.G24,A.G20 4 glyco-bond=---- sugar=3--3 groove=---- WC-->Major nts=4 GGGG B.G32,B.G20,B.G24,B.G29 step#3 mm(<>,outward) area=7.82 rise=3.34 twist=-56.4 Download PDB file Interactive view in 3Dmol.js
	4 glyco-bond=---- sugar=3--3 groove=---- WC-->Major nts=4 GGGG B.G32,B.G20,B.G24,B.G29 5 glyco-bond=---- sugar=333- groove=---- WC-->Major nts=4 GGGG B.G33,B.G21,B.G25,B.G30 step#4 pm(>>,forward) area=10.47 rise=3.35 twist=30.0 Download PDB file Interactive view in 3Dmol.js
	5 glyco-bond=---- sugar=333- groove=---- WC-->Major nts=4 GGGG B.G33,B.G21,B.G25,B.G30 6 glyco-bond=s--s sugar=---- groove=n-w- WC-->Major nts=4 GGGG B.G18,B.G22,B.G27,B.G35 step#5 pm(>>,forward) area=8.08 rise=3.50 twist=34.1 Download PDB file Interactive view in 3Dmol.js

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 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=10.71 rise=3.45 twist=30.1
  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

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Stem#2, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)

 1  glyco-bond=---- sugar=--33 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=10.47 rise=3.35 twist=30.0
  strand#1  U RNA glyco-bond=-- sugar=-3 nts=2 GG B.G20,B.G21
  strand#2  U RNA glyco-bond=-- sugar=-3 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