DSSR-enabled G4 identification/annotation: PDB entry 4wb2
Summary information and primary citation
- PDB-id
- 4wb2
- Class
- DNA-RNA hybrid
- Method
- X-ray (1.8 Å)
- Summary
- Crystal structure of the mirror-image l-RNA-l-DNA aptamer nox-d20 in complex with mouse c5a complement anaphylatoxin
- Reference
- Yatime L, Maasch C, Hoehlig K, Klussmann S, Andersen GR, Vater A (2015): "Structural basis for the targeting of complement anaphylatoxin C5a using a mixed L-RNA/L-DNA aptamer." Nat Commun, 6, 6481. doi: 10.1038/ncomms7481.
- Abstract
- L-Oligonucleotide aptamers (Spiegelmers) consist of non-natural L-configured nucleotides and are of particular therapeutic interest due to their high resistance to plasma nucleases. The anaphylatoxin C5a, a potent inflammatory mediator generated during complement activation that has been implicated with organ damage, can be efficiently targeted by Spiegelmers. Here, we present the first crystallographic structures of an active Spiegelmer, NOX-D20, bound to its physiological targets, mouse C5a and C5a-desArg. The structures reveal a complex 3D architecture for the L-aptamer that wraps around C5a, including an intramolecular G-quadruplex stabilized by a central Ca(2+) ion. Functional validation of the observed L-aptamer:C5a binding mode through mutational studies also rationalizes the specificity of NOX-D20 for mouse and human C5a against macaque and rat C5a. Finally, our structural model provides the molecular basis for the Spiegelmer affinity improvement through positional L-ribonucleotide to L-deoxyribonucleotide exchanges and for its inhibition of the C5a:C5aR interaction.
- G4 notes
- 2 G-tetrads, 1 G4 helix, 1 G4 stem, UUUU, parallel, 4+0, 2(-P-P-P)
Cartoon-block schematics in six views (download the tarball)
List of 2 G-tetrads
1 glyco-bond=---- sugar=.3.3 groove=---- planarity=0.404 type=saddle O+ nts=4 gggg 1:D.0G17,1:D.0G19,1:D.0G25,1:D.0G27 2 glyco-bond=---- sugar=-3-3 groove=---- planarity=0.327 type=other O+ nts=4 gggg 1:D.0G18,1:D.0G22,1:D.0G26,1:D.0G32
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, 2 G-tetrads, INTRA-molecular, with 1 stem
|
1 glyco-bond=---- sugar=.3.3 groove=---- WC-->Major O+ nts=4 gggg 1:D.0G17,1:D.0G19,1:D.0G25,1:D.0G27 2 glyco-bond=---- sugar=-3-3 groove=---- WC-->Major O+ nts=4 gggg 1:D.0G18,1:D.0G22,1:D.0G26,1:D.0G32 step#1 pm(>>,forward) area=7.02 rise=3.32 twist=50.2 strand#1 --- glyco-bond=-- sugar=.- nts=2 gg 1:D.0G17,1:D.0G18 strand#2 --- glyco-bond=-- sugar=33 nts=2 gg 1:D.0G19,1:D.0G22 strand#3 --- glyco-bond=-- sugar=.- nts=2 gg 1:D.0G25,1:D.0G26 strand#4 --- glyco-bond=-- sugar=33 nts=2 gg 1:D.0G27,1:D.0G32 |
| 1 stacking diagram | |
|
1 glyco-bond=---- sugar=.3.3 groove=---- WC-->Major O+ nts=4 gggg 1:D.0G17,1:D.0G19,1:D.0G25,1:D.0G27 |
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, 2 G-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, 4+0, 2(-P-P-P)
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1 glyco-bond=---- sugar=.3.3 groove=---- WC-->Major O+ nts=4 gggg 1:D.0G17,1:D.0G19,1:D.0G25,1:D.0G27 2 glyco-bond=---- sugar=-3-3 groove=---- WC-->Major O+ nts=4 gggg 1:D.0G18,1:D.0G22,1:D.0G26,1:D.0G32 step#1 pm(>>,forward) area=7.02 rise=3.32 twist=50.2 strand#1 U --- glyco-bond=-- sugar=.- nts=2 gg 1:D.0G17,1:D.0G18 strand#2* U --- glyco-bond=-- sugar=33 nts=2 gg 1:D.0G19,1:D.0G22 bulged-nts=2 uu 1:D.0U20,1:D.0U21 strand#3 U --- glyco-bond=-- sugar=.- nts=2 gg 1:D.0G25,1:D.0G26 strand#4* U --- glyco-bond=-- sugar=33 nts=2 gg 1:D.0G27,1:D.0G32 bulged-nts=4 uguc 1:D.3KA28,1:D.0G29,1:D.3KA30,1:D.0C31 loop#1 type=propeller strands=[#1,#2] nts=0 loop#2 type=propeller strands=[#2,#3] nts=2 uu 1:D.0U23,1:D.0U24 loop#3 type=propeller strands=[#3,#4] nts=0 |