› 4r8i

X-ray diffraction
2.05Å resolution

High Resolution Structure of a Mirror-Image RNA Oligonucleotide Aptamer in Complex with the Chemokine CCL2

Released:
DOI: 10.2210/pdb4r8i/pdb
PDB entry 4r8i coloured by chain, front view.
PDB entry 4r8i coloured by chain, side view.
PDB entry 4r8i coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structure of a mirror-image L-RNA aptamer (Spiegelmer) in complex with the natural L-protein target CCL2.
Oberthür D, Achenbach J, Gabdulkhakov A, Buchner K, Maasch C, Falke S, Rehders D, Klussmann S, Betzel C
Nat Commun 6 6923 (2015)
PMID: 25901662

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-146614 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
C-C motif chemokine 2 Chain: A
Molecule details ›
Chain: A
Length: 77 amino acids
Theoretical weight: 8.83 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P13500 (Residues: 24-99; Coverage: 100%)
Gene names: CCL2, MCP1, SCYA2
Sequence domains: Small cytokines (intecrine/chemokine), interleukin-8 like
Structure domains: OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Mirror-Image RNA Oligonucleotide Aptamer NOXE36 Chain: B
Molecule details ›
Chain: B
Length: 40 nucleotides
Theoretical weight: 12.91 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand NA 1 x NA
Ligand SR 1 x SR
Ligand K 5 x K
3 modified residues:
Ligand 0G 13 x 0G
Ligand 0C 14 x 0C
Ligand 0U 6 x 0U

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X13
Spacegroup: P43212
Unit cell:
a: 108.912Å b: 108.912Å c: 34.812Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.205 0.2 0.25
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

26 review citations

Aptamers as targeted therapeutics: current potential and challenges.
Zhou et al. (2017)
25 more

3 mentions without citation

Structural Biology for the Molecular Insight between Aptamers and Target Proteins.
Zhang et al. (2021)
2 more