› 4wb3

X-ray diffraction
2Å resolution

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

Released:
DOI: 10.2210/pdb4wb3/pdb
Model geometry
Fit model/data
PDB entry 4wb3 coloured by chain, front view.
PDB entry 4wb3 coloured by chain, side view.
PDB entry 4wb3 coloured by chain, top view.
Source organisms:
Primary publication:
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 GR, Vater A
OpenAccess logo Nat Commun 6 6481 (2015)
PMID: 25901944

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero dimer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-113165 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA/RNA hybrid molecule
Macromolecules (2 distinct):
C5a anaphylatoxin Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 78 amino acids
Theoretical weight: 8.89 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P06684 (Residues: 679-754; Coverage: 5%)
Gene names: C5, Hc
Sequence domains: Anaphylotoxin-like domain
Structure domains: Anaphylotoxins (complement system)
mixed L-RNA/L-DNA aptamer NOX-D20 (40-MER) Chains: D, E
Molecule details ›
Chains: D, E
Length: 40 nucleotides
Theoretical weight: 12.96 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand CA 6 x CA
Ligand ACT 3 x ACT
Ligand MG 2 x MG
6 modified residues:
Ligand 0G 36 x 0G
Ligand 0C 10 x 0C
Ligand 0U 14 x 0U
Ligand 0DG 2 x 0DG
Ligand 0DA 2 x 0DA
Ligand 0DC 2 x 0DC

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: MAX II BEAMLINE I911-3
Spacegroup: P21212
Unit cell:
a: 45.84Å b: 282.63Å c: 45.76Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.164 0.163 0.199
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

12 review citations

Embracing proteins: structural themes in aptamer-protein complexes.
Gelinas et al. (2016)
11 more

2 mentions without citation

Structural Insights into Protein-Aptamer Recognitions Emerged from Experimental and Computational Studies.
Troisi et al. (2023)
1 more