4R8I

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 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1038/ncomms7923

  • 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 protei ...

    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

    1] Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY Building 22a, Notkestrasse 85, 22607 Hamburg, Germany [2] Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron-DESY, Notkestrasse 85, 22607 Hamburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
C-C motif chemokine 2
A
77Homo sapiensMutation(s): 0 
Gene Names: CCL2 (MCP1, SCYA2)
Find proteins for P13500 (Homo sapiens)
Go to Gene View: CCL2
Go to UniProtKB:  P13500
Entity ID: 2
MoleculeChainsLengthOrganism
Mirror-Image RNA Oligonucleotide Aptamer NOXE36B40synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SR
Query on SR

Download SDF File 
Download CCD File 
B
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
0G
Query on 0G
B
L-RNA LINKINGC10 H14 N5 O8 P

--

0U1
Query on 0U1
B
L-RNA LINKINGC10 H15 N2 O8 P Se

--

0C
Query on 0C
B
L-RNA LINKINGC9 H14 N3 O8 P

--

0A
Query on 0A
B
L-RNA LINKINGC10 H14 N5 O7 P

--

0U
Query on 0U
B
L-RNA LINKINGC9 H13 N2 O9 P

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.200 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 108.912α = 90.00
b = 108.912β = 90.00
c = 34.812γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
PHENIXmodel building
MxCuBEdata collection
XDSdata reduction
REFMACrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-29
    Type: Initial release
  • Version 1.1: 2015-05-06
    Type: Database references