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URL: https://www.rcsb.org/structure/4R8I

⇱ RCSB PDB - 4R8I: High Resolution Structure of a Mirror-Image RNA Oligonucleotide Aptamer in Complex with the Chemokine CCL2

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Structures from the PDB archive		1,062,058
Computed Structure Models (CSM)

 4R8I | pdb_00004r8i

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.250 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

This is version 1.2 of the entry. See complete history. 

Literature

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., Buchner, K., Maasch, C., Falke, S., Rehders, D., Klussmann, S., Betzel, C.

(2015) Nat Commun 6: 6923-6923

  • DOI: https://doi.org/10.1038/ncomms7923
  • Primary Citation Related Structures: 
    4R8I

  • PubMed Abstract: 

    We report the crystal structure of a 40 mer mirror-image RNA oligonucleotide completely built from nucleotides of the non-natural L-chirality in complex with the pro-inflammatory chemokine L-CLL2 (monocyte chemoattractant protein-1), a natural protein composed of regular L-amino acids. The L-oligonucleotide is an L-aptamer (a Spiegelmer) identified to bind L-CCL2 with high affinity, thereby neutralizing the chemokine's activity. CCL2 plays a key role in attracting and positioning monocytes; its overexpression in several inflammatory diseases makes CCL2 an interesting pharmacological target. The PEGylated form of the L-aptamer, NOX-E36 (emapticap pegol), already showed promising efficacy in clinical Phase II studies conducted in diabetic nephropathy patients. The structure of the L-oligonucleotide[Symbol: see text]L-protein complex was solved and refined to 2.05 Å. It unveils the L-aptamer's intramolecular contacts and permits a detailed analysis of its structure-function relationship. Furthermore, the analysis of the intermolecular drug-target interactions reveals insight into the selectivity of the L-aptamer for certain related chemokines.

    • Organizational Affiliation: 
    • Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY Building 22a, Notkestrasse 85, 22607 Hamburg, Germany.
    • Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron-DESY, Notkestrasse 85, 22607 Hamburg, Germany.
    • NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany.
    • Institute of Protein Research, RAS, Pushchino, Moscow Region 142290, Russian Federation.

Macromolecule Content 

  • Total Structure Weight: 22.05 kDa 
  • Atom Count: 1,515 
  • Modeled Residue Count: 108 
  • Deposited Residue Count: 117 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
C-C motif chemokine 277Homo sapiensMutation(s): 0 
Gene Names: CCL2, MCP1, SCYA2
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UniProt & NIH Common Fund Data Resources
Find proteins for P13500 (Homo sapiens)
Explore P13500 
Go to UniProtKB:  P13500
PHAROS:  P13500
GTEx:  ENSG00000108691 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13500
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 2
MoleculeChains LengthOrganismImage
Mirror-Image RNA Oligonucleotide Aptamer NOXE3640synthetic construct👁 Image
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.250 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.912α = 90
b = 108.912β = 90
c = 34.812γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
PHENIXmodel building
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-29
    Type: Initial release
  • Version 1.1: 2015-05-06
    Changes: Database references
  • Version 1.2: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.