4WB3

Crystal structure of the mirror-image L-RNA/L-DNA aptamer NOX-D20 in complex with mouse C5a-desArg complement anaphylatoxin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for the targeting of complement anaphylatoxin C5a using a mixed L-RNA/L-DNA aptamer.

Yatime, L.Maasch, C.Hoehlig, K.Klussmann, S.Andersen, G.R.Vater, A.

(2015) Nat Commun 6: 6481-6481

  • DOI: 10.1038/ncomms7481
  • Primary Citation of Related Structures:  

  • PubMed 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 duri ...

    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.


    Organizational Affiliation

    NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany.,Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Complement C5
A, B, C
78Mus musculusMutation(s): 0 
Gene Names: C5 (Hc)
Find proteins for P06684 (Mus musculus)
Go to Gene View: C5
Go to UniProtKB:  P06684
Entity ID: 2
MoleculeChainsLengthOrganism
mixed L-RNA/L-DNA aptamer NOX-D20 (40-MER)D,E40synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
B, D
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, C, D, E
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
D, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  8 Unique
IDChainsTypeFormula2D DiagramParent
0G
Query on 0G
D, E
L-RNA LINKINGC10 H14 N5 O8 P

--

0C
Query on 0C
D, E
L-RNA LINKINGC9 H14 N3 O8 P

--

0A
Query on 0A
D, E
L-RNA LINKINGC10 H14 N5 O7 P

--

0DG
Query on 0DG
D, E
L-DNA LINKINGC10 H14 N5 O7 P

--

0DA
Query on 0DA
D, E
L-DNA LINKINGC10 H14 N5 O6 P

--

0U
Query on 0U
D, E
L-RNA LINKINGC9 H13 N2 O9 P

--

3KA
Query on 3KA
D, E
NON-POLYMERC9 H13 N2 O8 P

--

0DC
Query on 0DC
D, E
L-DNA LINKINGC9 H14 N3 O7 P

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.163 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 45.840α = 90.00
b = 282.630β = 90.00
c = 45.760γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
XSCALEdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-06
    Type: Initial release
  • Version 1.1: 2018-01-17
    Type: Data collection