DSSR-enabled G4 identification/annotation: PDB entry 7zkm
Summary information and primary citation
- PDB-id
- 7zkm
- Class
- hydrolase
- Method
- X-ray (2.0 Å)
- Summary
- X-ray structure of the complex between human alpha thrombin and a pseudo-cyclic thrombin binding aptamer (tba-nnp-ddp) - crystal form beta
- Reference
- Troisi R, Riccardi C, Perez de Carvasal K, Smietana M, Morvan F, Del Vecchio P, Montesarchio D, Sica F (2022): "A terminal functionalization strategy reveals unusual binding abilities of anti-thrombin anticoagulant aptamers." Mol Ther Nucleic Acids, 30, 585-594. doi: 10.1016/j.omtn.2022.11.007.
- Abstract
- Despite their unquestionable properties, oligonucleotide aptamers display some drawbacks that continue to hinder their applications. Several strategies have been undertaken to overcome these weaknesses, using thrombin binding aptamers as proof-of-concept. In particular, the functionalization of a thrombin exosite I binding aptamer (TBA) with aromatic moieties, e.g., naphthalene dimides (N) and dialkoxynaphthalenes (D), attached at the 5' and 3' ends, respectively, proved to be highly promising. To obtain a molecular view of the effects of these modifications on aptamers, we performed a crystallographic analysis of one of these engineered oligonucleotides (TBA-NNp/DDp) in complex with thrombin. Surprisingly, three of the four examined crystallographic structures are ternary complexes in which thrombin binds a TBA-NNp/DDp molecule at exosite II as well as at exosite I, highlighting the ability of this aptamer, differently from unmodified TBA, to also recognize a localized region of exosite II. This novel ability is strictly related to the solvophobic behavior of the terminal modifications. Studies were also performed in solution to examine the properties of TBA-NNp/DDp in a crystal-free environment. The present results throw new light on the importance of appendages inducing a <i>pseudo</i>-cyclic charge-transfer structure in nucleic acid-based ligands to improve the interactions with proteins, thus considerably widening their potentialities.
- G4 notes
- 4 G-tetrads, 2 G4 helices, 2 G4 stems, UDUD, anti-parallel:chair, 2+2, 2(+Ln+Ln); UDUD, anti-parallel:chair, 2+2, 2(+Ln+Lw+Ln)
Cartoon-block schematics in six views (download the tarball)
List of 4 G-tetrads
1 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.296 type=other O+ nts=4 GGGG A.DG1,A.DG15,A.DG10,A.DG6 2 glyco-bond=-s-s sugar=3--- groove=wnwn planarity=0.298 type=bowl-2 O- nts=4 GGGG A.DG2,A.DG14,A.DG11,A.DG5 3 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.220 type=saddle O+ nts=4 GGGG B.DG1,B.DG15,B.DG10,B.DG6 4 glyco-bond=-s-s sugar=---- groove=wnwn planarity=0.305 type=bowl O- nts=4 GGGG B.DG2,B.DG14,B.DG11,B.DG5
List of 2 G4-helices
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=s-s- sugar=---- groove=wnwn Major-->WC O+ nts=4 GGGG A.DG1,A.DG15,A.DG10,A.DG6 2 glyco-bond=-s-s sugar=3--- groove=wnwn WC-->Major O- nts=4 GGGG A.DG2,A.DG14,A.DG11,A.DG5 step#1 mm(<>,outward) area=17.87 rise=3.48 twist=15.8 strand#1 DNA glyco-bond=s- sugar=-3 nts=2 GG A.DG1,A.DG2 strand#2 DNA glyco-bond=-s sugar=-- nts=2 GG A.DG15,A.DG14 strand#3 DNA glyco-bond=s- sugar=-- nts=2 GG A.DG10,A.DG11 strand#4 DNA glyco-bond=-s sugar=-- nts=2 GG A.DG6,A.DG5 |
| 1 stacking diagram | |
|
1 glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC O+ nts=4 GGGG A.DG1,A.DG15,A.DG10,A.DG6 |
Helix#2, 2 G-tetrads, INTRA-molecular, with 1 stem
|
1 glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC O+ nts=4 GGGG B.DG1,B.DG15,B.DG10,B.DG6 2 glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major O- nts=4 GGGG B.DG2,B.DG14,B.DG11,B.DG5 step#1 mm(<>,outward) area=15.93 rise=3.50 twist=16.2 strand#1 DNA glyco-bond=s- sugar=-- nts=2 GG B.DG1,B.DG2 strand#2 DNA glyco-bond=-s sugar=-- nts=2 GG B.DG15,B.DG14 strand#3 DNA glyco-bond=s- sugar=-- nts=2 GG B.DG10,B.DG11 strand#4 DNA glyco-bond=-s sugar=-- nts=2 GG B.DG6,B.DG5 |
| 1 stacking diagram | |
|
1 glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC O+ nts=4 GGGG B.DG1,B.DG15,B.DG10,B.DG6 |
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-tetrads, 2 loops, INTRA-molecular, UDUD, anti-parallel:chair, 2+2, 2(+Ln+Ln)
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1 glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC O+ nts=4 GGGG A.DG1,A.DG15,A.DG10,A.DG6 2 glyco-bond=-s-s sugar=3--- groove=wnwn WC-->Major O- nts=4 GGGG A.DG2,A.DG14,A.DG11,A.DG5 step#1 mm(<>,outward) area=17.87 rise=3.48 twist=15.8 strand#1 U DNA glyco-bond=s- sugar=-3 nts=2 GG A.DG1,A.DG2 strand#2 D DNA glyco-bond=-s sugar=-- nts=2 GG A.DG15,A.DG14 strand#3 U DNA glyco-bond=s- sugar=-- nts=2 GG A.DG10,A.DG11 strand#4 D DNA glyco-bond=-s sugar=-- nts=2 GG A.DG6,A.DG5 loop#1 type=lateral strands=[#1,#4] nts=2 TT A.DT3,A.DT4 loop#2 type=lateral strands=[#3,#2] nts=2 TT A.DT12,A.DT13 |
Stem#2, 2 G-tetrads, 3 loops, INTRA-molecular, UDUD, anti-parallel:chair, 2+2, 2(+Ln+Lw+Ln)
|
1 glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC O+ nts=4 GGGG B.DG1,B.DG15,B.DG10,B.DG6 2 glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major O- nts=4 GGGG B.DG2,B.DG14,B.DG11,B.DG5 step#1 mm(<>,outward) area=15.93 rise=3.50 twist=16.2 strand#1 U DNA glyco-bond=s- sugar=-- nts=2 GG B.DG1,B.DG2 strand#2 D DNA glyco-bond=-s sugar=-- nts=2 GG B.DG15,B.DG14 strand#3 U DNA glyco-bond=s- sugar=-- nts=2 GG B.DG10,B.DG11 strand#4 D DNA glyco-bond=-s sugar=-- nts=2 GG B.DG6,B.DG5 loop#1 type=lateral strands=[#1,#4] nts=2 TT B.DT3,B.DT4 loop#2 type=lateral strands=[#4,#3] nts=3 TGT B.DT7,B.DG8,B.DT9 loop#3 type=lateral strands=[#3,#2] nts=2 TT B.DT12,B.DT13 |