Summary information

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
4 G-tetrads, 2 G4 helices, 2 G4 stems, 2(-P-P-P), parallel(4+0), UUUU

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 4 G-tetrads

 1 glyco-bond=---- sugar=.3.3 groove=---- planarity=0.404 type=saddle nts=4 gggg D.0G17,D.0G19,D.0G25,D.0G27
 2 glyco-bond=---- sugar=-3-3 groove=---- planarity=0.327 type=other  nts=4 gggg D.0G18,D.0G22,D.0G26,D.0G32
 3 glyco-bond=---- sugar=.3.3 groove=---- planarity=0.336 type=other  nts=4 gggg E.0G17,E.0G19,E.0G25,E.0G27
 4 glyco-bond=---- sugar=-3-3 groove=---- planarity=0.336 type=other  nts=4 gggg E.0G18,E.0G22,E.0G26,E.0G32

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-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=---- sugar=.3.3 groove=---- WC-->Major nts=4 gggg D.0G17,D.0G19,D.0G25,D.0G27
 2  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 gggg D.0G18,D.0G22,D.0G26,D.0G32
  step#1  pm(>>,forward)  area=7.02  rise=3.32 twist=50.2
  strand#1 --- glyco-bond=-- sugar=.- nts=2 gg D.0G17,D.0G18
  strand#2 --- glyco-bond=-- sugar=33 nts=2 gg D.0G19,D.0G22
  strand#3 --- glyco-bond=-- sugar=.- nts=2 gg D.0G25,D.0G26
  strand#4 --- glyco-bond=-- sugar=33 nts=2 gg D.0G27,D.0G32

Download PDB file
Interactive view in 3Dmol.js
1 stacking diagram 
 1  glyco-bond=---- sugar=.3.3 groove=---- WC-->Major nts=4 gggg D.0G17,D.0G19,D.0G25,D.0G27
 2  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 gggg D.0G18,D.0G22,D.0G26,D.0G32
  step#1  pm(>>,forward)  area=7.02  rise=3.32 twist=50.2

Download PDB file
Interactive view in 3Dmol.js

Helix#2, 2 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=---- sugar=.3.3 groove=---- WC-->Major nts=4 gggg E.0G17,E.0G19,E.0G25,E.0G27
 2  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 gggg E.0G18,E.0G22,E.0G26,E.0G32
  step#1  pm(>>,forward)  area=7.19  rise=3.31 twist=49.8
  strand#1 --- glyco-bond=-- sugar=.- nts=2 gg E.0G17,E.0G18
  strand#2 --- glyco-bond=-- sugar=33 nts=2 gg E.0G19,E.0G22
  strand#3 --- glyco-bond=-- sugar=.- nts=2 gg E.0G25,E.0G26
  strand#4 --- glyco-bond=-- sugar=33 nts=2 gg E.0G27,E.0G32

Download PDB file
Interactive view in 3Dmol.js
1 stacking diagram 
 1  glyco-bond=---- sugar=.3.3 groove=---- WC-->Major nts=4 gggg E.0G17,E.0G19,E.0G25,E.0G27
 2  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 gggg E.0G18,E.0G22,E.0G26,E.0G32
  step#1  pm(>>,forward)  area=7.19  rise=3.31 twist=49.8

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

 1  glyco-bond=---- sugar=.3.3 groove=---- WC-->Major nts=4 gggg D.0G17,D.0G19,D.0G25,D.0G27
 2  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 gggg D.0G18,D.0G22,D.0G26,D.0G32
  step#1  pm(>>,forward)  area=7.02  rise=3.32 twist=50.2
  strand#1  U --- glyco-bond=-- sugar=.- nts=2 gg D.0G17,D.0G18
  strand#2* U --- glyco-bond=-- sugar=33 nts=2 gg D.0G19,D.0G22 bulged-nts=2 uu D.0U20,D.0U21
  strand#3  U --- glyco-bond=-- sugar=.- nts=2 gg D.0G25,D.0G26
  strand#4* U --- glyco-bond=-- sugar=33 nts=2 gg D.0G27,D.0G32 bulged-nts=4 uguc D.3KA28,D.0G29,D.3KA30,D.0C31
  loop#1 type=propeller strands=[#1,#2] nts=0
  loop#2 type=propeller strands=[#2,#3] nts=2 uu D.0U23,D.0U24
  loop#3 type=propeller strands=[#3,#4] nts=0

Download PDB file
Interactive view in 3Dmol.js

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

 1  glyco-bond=---- sugar=.3.3 groove=---- WC-->Major nts=4 gggg E.0G17,E.0G19,E.0G25,E.0G27
 2  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major nts=4 gggg E.0G18,E.0G22,E.0G26,E.0G32
  step#1  pm(>>,forward)  area=7.19  rise=3.31 twist=49.8
  strand#1  U --- glyco-bond=-- sugar=.- nts=2 gg E.0G17,E.0G18
  strand#2* U --- glyco-bond=-- sugar=33 nts=2 gg E.0G19,E.0G22 bulged-nts=2 uu E.0U20,E.0U21
  strand#3  U --- glyco-bond=-- sugar=.- nts=2 gg E.0G25,E.0G26
  strand#4* U --- glyco-bond=-- sugar=33 nts=2 gg E.0G27,E.0G32 bulged-nts=4 uguc E.3KA28,E.0G29,E.3KA30,E.0C31
  loop#1 type=propeller strands=[#1,#2] nts=0
  loop#2 type=propeller strands=[#2,#3] nts=2 uu E.0U23,E.0U24
  loop#3 type=propeller strands=[#3,#4] nts=0

Download PDB file
Interactive view in 3Dmol.js