4R8I: Mirror-Image RNA Oligonucleotide Aptamer

High Resolution Structure of a Mirror-Image RNA Oligonucleotide Aptamer in Complex with the Chemokine CCL2. Determined by X-ray diffraction at 2.05 Å resolution. Released 29 Apr 2015.

Method: X-ray diffraction
Resolution: 2.05 Å
Organisms: Homo sapiens, synthetic construct
Chains: 2
Atoms: 1,515
Mol. weight: 22.05 kDa
Ligands: SR
Released: 29 Apr 2015

Explore 4R8I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4R8I contains 2 α-helices and 3 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	22-24	3
β-strand	25-31	7	1
β-strand	40-45	6	1
β-strand	50-53	4	1
α-helix	58-69	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
C-C motif chemokine 2	A	protein	77	Homo sapiens	P13500 (AlphaFold model)
Mirror-Image RNA Oligonucleotide Aptamer NOXE36	B	RNA	40	synthetic construct

Sequence of entity 1 (A), FASTA

>4R8I_1 C-C motif chemokine 2 (chains A)
MQPDAINAPVTCCYNFTNRKISVQRLASYRRITSSKCPKEAVIFKTIVAKEICADPKQKW
VQDSMDHLDKQTQTPKT

Sequence of entity 2 (B), FASTA

>4R8I_2 Mirror-Image RNA Oligonucleotide Aptamer NOXE36 (chains B)
GCXCGUCCCUCXCCGGUGCXXGUGXXGCCGXGGCUCUGCG

Ligands and cofactors

ID	Name	Formula	Copies
SR	Strontium ion	Sr	1

Water and common crystallization additives (NA, K) are not listed.

Primary citation

Crystal structure of a mirror-image L-RNA aptamer (Spiegelmer) in complex with the natural L-protein target CCL2. Oberthur, D., Achenbach, J., Gabdulkhakov, A. et al. Nat Commun (2015) 6:6923-6923. DOI 10.1038/ncomms7923 · PubMed

Other PDB entries of the same protein (UniProt P13500 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7SO0 1.74 Å, Crystal Structure of the Engineered Tick Evasin EVA-P974(F31A) Complexed to Human…
1DOK 1.85 Å, Monocyte chemoattractant protein 1, P-form
3IFD 1.9 Å, Human synthetic monocyte chemoattractant protein 1 (MCP-1)
1DOL 2.4 Å, Monocyte chemoattractant protein 1, I-form
2NZ1 2.5 Å, Viral Chemokine Binding Protein M3 From Murine Gammaherpesvirus68 In Complex With The…
2BDN 2.53 Å, Crystal structure of human MCP-1 bound to a blocking antibody, 11K2
4ZK9 2.6 Å, The chemokine binding protein of orf virus complexed with CCL2
1ML0 2.8 Å, Viral chemokine binding protein M3 from murine GAMMAHERPESVIRUS68 in complex with the…
4DN4 2.8 Å, Crystal structure of the complex between cnto888 fab and mcp-1 mutant p8a
7XA3 2.9 Å, Cryo-EM structure of the CCL2 bound CCR2-Gi complex
8FJ0 2.91 Å, Crystal Structure of the Tick Evasin EVA-AAM1001(Y44A) Complexed to Human Chemokine CCL2
1DOM Solution structure of the monocyte chemoattractant protein-1 dimer using heteronuclear,…

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