DSSR-curated G4 structure: PDB entry 5v3f

Summary information

PDB id: 5v3f
Class: RNA
Method: X-ray (1.7 Å)
Summary: Co-crystal structure of the fluorogenic RNA mango
Reference: Trachman RJ, Demeshkina NA, Lau MWL, Panchapakesan SSS, Jeng SCY, Unrau PJ, Ferre-D'Amare AR (2017): "Structural basis for high-affinity fluorophore binding and activation by RNA Mango." Nat. Chem. Biol., 13, 807-813. doi: 10.1038/nchembio.2392.
Abstract: Genetically encoded fluorescent protein tags have revolutionized proteome studies, whereas the lack of intrinsically fluorescent RNAs has hindered transcriptome exploration. Among several RNA-fluorophore complexes that potentially address this problem, RNA Mango has an exceptionally high affinity for its thiazole orange (TO)-derived fluorophore, TO1-Biotin (K_d ∼3 nM), and, in complex with related ligands, it is one of the most redshifted fluorescent macromolecular tags known. To elucidate how this small aptamer exhibits such properties, which make it well suited for studying low-copy cellular RNAs, we determined its 1.7-Å-resolution co-crystal structure. Unexpectedly, the entire ligand, including TO, biotin and the linker connecting them, abuts one of the near-planar faces of the three-tiered G-quadruplex. The two heterocycles of TO are held in place by two loop adenines and form a 45° angle with respect to each other. Minimizing this angle would increase quantum yield and further improve this tool for in vivo RNA visualization.
G4 notes: 6 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack, 3(-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=---- sugar=-3-3 groove=---- planarity=0.339 type=bowl-2 nts=4 GGGG A.G8,A.G13,A.G18,A.G23
 2 glyco-bond=---- sugar=3333 groove=---- planarity=0.185 type=saddle nts=4 GGGG A.G9,A.G14,A.G19,A.G24
 3 glyco-bond=s--- sugar=---- groove=w--n planarity=0.283 type=other  nts=4 GGGG A.G10,A.G16,A.G21,A.G26
 4 glyco-bond=---- sugar=-3-3 groove=---- planarity=0.349 type=bowl-2 nts=4 GGGG B.G8,B.G13,B.G18,B.G23
 5 glyco-bond=---- sugar=3333 groove=---- planarity=0.182 type=saddle nts=4 GGGG B.G9,B.G14,B.G19,B.G24
 6 glyco-bond=s--- sugar=---- groove=w--n planarity=0.283 type=other  nts=4 GGGG B.G10,B.G16,B.G21,B.G26

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=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.G10,A.G16,A.G21,A.G26 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G9,A.G14,A.G19,A.G24 3* glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GGGG A.G8,A.G13,A.G18,A.G23 4 glyco-bond=---- sugar=3-3- groove=---- Major-->WC nts=4 GGGG B.G13,B.G8,B.G23,B.G18 5 glyco-bond=---- sugar=3333 groove=---- Major-->WC nts=4 GGGG B.G14,B.G9,B.G24,B.G19 6 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG B.G16,B.G10,B.G26,B.G21 step#1 pp(><,inward) area=26.53 rise=3.42 twist=28.5 step#2 mp(<<,backward) area=8.06 rise=3.26 twist=34.3 step#3 mm(<>,outward) area=24.36 rise=3.59 twist=0.3 step#4 pm(>>,forward) area=8.59 rise=3.28 twist=34.0 step#5 pp(><,inward) area=27.13 rise=3.43 twist=27.8 strand#1 RNA glyco-bond=s----- sugar=-3-33- nts=6 GGGGGG A.G10,A.G9,A.G8,B.G13,B.G14,B.G16 strand#2 RNA glyco-bond=-----s sugar=-33-3- nts=6 GGGGGG A.G16,A.G14,A.G13,B.G8,B.G9,B.G10 strand#3 RNA glyco-bond=------ sugar=-3-33- nts=6 GGGGGG A.G21,A.G19,A.G18,B.G23,B.G24,B.G26 strand#4 RNA glyco-bond=------ sugar=-33-3- nts=6 GGGGGG A.G26,A.G24,A.G23,B.G18,B.G19,B.G21 Download PDB file Interactive view in 3Dmol.js
5 stacking diagrams
	1 glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.G10,A.G16,A.G21,A.G26 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G9,A.G14,A.G19,A.G24 step#1 pp(><,inward) area=26.53 rise=3.42 twist=28.5 Download PDB file Interactive view in 3Dmol.js
	2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G9,A.G14,A.G19,A.G24 3* glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GGGG A.G8,A.G13,A.G18,A.G23 step#2 mp(<<,backward) area=8.06 rise=3.26 twist=34.3 Download PDB file Interactive view in 3Dmol.js
	3* glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GGGG A.G8,A.G13,A.G18,A.G23 4 glyco-bond=---- sugar=3-3- groove=---- Major-->WC nts=4 GGGG B.G13,B.G8,B.G23,B.G18 step#3 mm(<>,outward) area=24.36 rise=3.59 twist=0.3 Download PDB file Interactive view in 3Dmol.js
	4 glyco-bond=---- sugar=3-3- groove=---- Major-->WC nts=4 GGGG B.G13,B.G8,B.G23,B.G18 5 glyco-bond=---- sugar=3333 groove=---- Major-->WC nts=4 GGGG B.G14,B.G9,B.G24,B.G19 step#4 pm(>>,forward) area=8.59 rise=3.28 twist=34.0 Download PDB file Interactive view in 3Dmol.js
	5 glyco-bond=---- sugar=3333 groove=---- Major-->WC nts=4 GGGG B.G14,B.G9,B.G24,B.G19 6 glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major nts=4 GGGG B.G16,B.G10,B.G26,B.G21 step#5 pp(><,inward) area=27.13 rise=3.43 twist=27.8 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, 3 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 3(-P-P-P), parallel(4+0)

 1  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GGGG A.G8,A.G13,A.G18,A.G23
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG A.G9,A.G14,A.G19,A.G24
 3  glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG A.G10,A.G16,A.G21,A.G26
  step#1  pm(>>,forward)  area=8.06  rise=3.26 twist=34.3
  step#2  pp(><,inward)   area=26.53 rise=3.42 twist=28.5
  strand#1  U RNA glyco-bond=--s sugar=-3- nts=3 GGG A.G8,A.G9,A.G10
  strand#2* U RNA glyco-bond=--- sugar=33- nts=3 GGG A.G13,A.G14,A.G16 bulged-nts=1 U A.U15
  strand#3* U RNA glyco-bond=--- sugar=-3- nts=3 GGG A.G18,A.G19,A.G21 bulged-nts=1 A A.A20
  strand#4* U RNA glyco-bond=--- sugar=33- nts=3 GGG A.G23,A.G24,A.G26 bulged-nts=1 A A.A25
  loop#1 type=propeller strands=[#1,#2] nts=2 AC A.A11,A.C12
  loop#2 type=propeller strands=[#2,#3] nts=1 C A.C17
  loop#3 type=propeller strands=[#3,#4] nts=1 A A.A22

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Interactive view in 3Dmol.js

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

 1  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 GGGG B.G8,B.G13,B.G18,B.G23
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG B.G9,B.G14,B.G19,B.G24
 3  glyco-bond=s--- sugar=---- groove=w--n Major-->WC nts=4 GGGG B.G10,B.G16,B.G21,B.G26
  step#1  pm(>>,forward)  area=8.59  rise=3.28 twist=34.0
  step#2  pp(><,inward)   area=27.13 rise=3.43 twist=27.8
  strand#1  U RNA glyco-bond=--s sugar=-3- nts=3 GGG B.G8,B.G9,B.G10
  strand#2* U RNA glyco-bond=--- sugar=33- nts=3 GGG B.G13,B.G14,B.G16 bulged-nts=1 U B.U15
  strand#3* U RNA glyco-bond=--- sugar=-3- nts=3 GGG B.G18,B.G19,B.G21 bulged-nts=1 A B.A20
  strand#4* U RNA glyco-bond=--- sugar=33- nts=3 GGG B.G23,B.G24,B.G26 bulged-nts=1 A B.A25
  loop#1 type=propeller strands=[#1,#2] nts=2 AC B.A11,B.C12
  loop#2 type=propeller strands=[#2,#3] nts=1 C B.C17
  loop#3 type=propeller strands=[#3,#4] nts=1 A B.A22