DSSR-enabled G4 identification/annotation: PDB entry 6c63
Summary information and primary citation
- PDB-id
- 6c63
- Class
- RNA
- Method
- X-ray (2.9 Å)
- Summary
- Crystal structure of the mango-ii fluorescent aptamer bound to to1-biotin
- Reference
- Trachman 3rd RJ, Abdolahzadeh A, Andreoni A, Cojocaru R, Knutson JR, Ryckelynck M, Unrau PJ, Ferre-D'Amare AR (2018): "Crystal Structures of the Mango-II RNA Aptamer Reveal Heterogeneous Fluorophore Binding and Guide Engineering of Variants with Improved Selectivity and Brightness." Biochemistry, 57, 3544-3548. doi: 10.1021/acs.biochem.8b00399.
- Abstract
- Several RNA aptamers that bind small molecules and enhance their fluorescence have been successfully used to tag and track RNAs in vivo, but these genetically encodable tags have not yet achieved single-fluorophore resolution. Recently, Mango-II, an RNA that binds TO1-Biotin with ∼1 nM affinity and enhances its fluorescence by >1500-fold, was isolated by fluorescence selection from the pool that yielded the original RNA Mango. We determined the crystal structures of Mango-II in complex with two fluorophores, TO1-Biotin and TO3-Biotin, and found that despite their high affinity, the ligands adopt multiple distinct conformations, indicative of a binding pocket with modest stereoselectivity. Mutational analysis of the binding site led to Mango-II(A22U), which retains high affinity for TO1-Biotin but now discriminates >5-fold against TO3-biotin. Moreover, fluorescence enhancement of TO1-Biotin increases by 18%, while that of TO3-Biotin decreases by 25%. Crystallographic, spectroscopic, and analogue studies show that the A22U mutation improves conformational homogeneity and shape complementarity of the fluorophore-RNA interface. Our work demonstrates that even after extensive functional selection, aptamer RNAs can be further improved through structure-guided engineering.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem, UUUU, parallel, 4+0, 3(-P-P-P)
Cartoon-block schematics in six views (download the tarball)
List of 3 G-tetrads
1 glyco-bond=---- sugar=-333 groove=---- planarity=0.245 type=other O+ nts=4 GGGG 1:A.G10,1:A.G15,1:A.G20,1:A.G26 2 glyco-bond=---- sugar=3333 groove=---- planarity=0.106 type=planar O+ nts=4 GGGG 1:A.G11,1:A.G16,1:A.G21,1:A.G27 3 glyco-bond=---- sugar=---- groove=---- planarity=0.088 type=planar O- nts=4 GGGG 1:A.G13,1:A.G29,1:A.G24,1: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, 3 G-tetrads, INTRA-molecular, with 1 stem
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1 glyco-bond=---- sugar=-333 groove=---- WC-->Major O+ nts=4 GGGG 1:A.G10,1:A.G15,1:A.G20,1:A.G26 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG 1:A.G11,1:A.G16,1:A.G21,1:A.G27 3 glyco-bond=---- sugar=---- groove=---- Major-->WC O- nts=4 GGGG 1:A.G13,1:A.G18,1:A.G24,1:A.G29 step#1 pm(>>,forward) area=9.15 rise=3.32 twist=32.9 step#2 pp(><,inward) area=27.20 rise=3.39 twist=29.0 strand#1 RNA glyco-bond=--- sugar=-3- nts=3 GGG 1:A.G10,1:A.G11,1:A.G13 strand#2 RNA glyco-bond=--- sugar=33- nts=3 GGG 1:A.G15,1:A.G16,1:A.G18 strand#3 RNA glyco-bond=--- sugar=33- nts=3 GGG 1:A.G20,1:A.G21,1:A.G24 strand#4 RNA glyco-bond=--- sugar=33- nts=3 GGG 1:A.G26,1:A.G27,1:A.G29 |
| 2 stacking diagrams | |
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1 glyco-bond=---- sugar=-333 groove=---- WC-->Major O+ nts=4 GGGG 1:A.G10,1:A.G15,1:A.G20,1:A.G26 |
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2 glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG 1:A.G11,1:A.G16,1:A.G21,1:A.G27 |
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-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, 4+0, 3(-P-P-P)
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1 glyco-bond=---- sugar=-333 groove=---- WC-->Major O+ nts=4 GGGG 1:A.G10,1:A.G15,1:A.G20,1:A.G26 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major O+ nts=4 GGGG 1:A.G11,1:A.G16,1:A.G21,1:A.G27 3 glyco-bond=---- sugar=---- groove=---- Major-->WC O- nts=4 GGGG 1:A.G13,1:A.G18,1:A.G24,1:A.G29 step#1 pm(>>,forward) area=9.15 rise=3.32 twist=32.9 step#2 pp(><,inward) area=27.20 rise=3.39 twist=29.0 strand#1* U RNA glyco-bond=--- sugar=-3- nts=3 GGG 1:A.G10,1:A.G11,1:A.G13 bulged-nts=1 A 1:A.A12 strand#2* U RNA glyco-bond=--- sugar=33- nts=3 GGG 1:A.G15,1:A.G16,1:A.G18 bulged-nts=1 A 1:A.A17 strand#3* U RNA glyco-bond=--- sugar=33- nts=3 GGG 1:A.G20,1:A.G21,1:A.G24 bulged-nts=2 AA 1:A.A22,1:A.A23 strand#4* U RNA glyco-bond=--- sugar=33- nts=3 GGG 1:A.G26,1:A.G27,1:A.G29 bulged-nts=1 A 1:A.A28 loop#1 type=propeller strands=[#1,#2] nts=1 A 1:A.A14 loop#2 type=propeller strands=[#2,#3] nts=1 A 1:A.A19 loop#3 type=propeller strands=[#3,#4] nts=1 A 1:A.A25 |