4XW2

Structural basis for simvastatin competitive antagonism of complement receptor 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.001 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Basis for Simvastatin Competitive Antagonism of Complement Receptor 3.

Jensen, M.R.Bajic, G.Zhang, X.Laustsen, A.K.Kolds, H.Skeby, K.K.Schitt, B.Andersen, G.R.Vorup-Jensen, T.

(2016) J.Biol.Chem. 291: 16963-16976

  • DOI: 10.1074/jbc.M116.732222

  • PubMed Abstract: 
  • The complement system is an important part of the innate immune response to infection but may also cause severe complications during inflammation. Small molecule antagonists to complement receptor 3 (CR3) have been widely sought, but a structural bas ...

    The complement system is an important part of the innate immune response to infection but may also cause severe complications during inflammation. Small molecule antagonists to complement receptor 3 (CR3) have been widely sought, but a structural basis for their mode of action is not available. We report here on the structure of the human CR3 ligand-binding I domain in complex with simvastatin. Simvastatin targets the metal ion-dependent adhesion site of the open, ligand-binding conformation of the CR3 I domain by direct contact with the chelated Mg(2+) ion. Simvastatin antagonizes I domain binding to the complement fragments iC3b and C3d but not to intercellular adhesion molecule-1. By virtue of the I domain's wide distribution in binding kinetics to ligands, it was possible to identify ligand binding kinetics as discriminator for simvastatin antagonism. In static cellular experiments, 15-25 μm simvastatin reduced adhesion by K562 cells expressing recombinant CR3 and by primary human monocytes, with an endogenous expression of this receptor. Application of force to adhering monocytes potentiated the effects of simvastatin where only a 50-100 nm concentration of the drug reduced the adhesion by 20-40% compared with untreated cells. The ability of simvastatin to target CR3 in its ligand binding-activated conformation is a novel mechanism to explain the known anti-inflammatory effects of this compound, in particular because this CR3 conformation is found in pro-inflammatory environments. Our report points to new designs of CR3 antagonists and opens new perspectives and identifies druggable receptors from characterization of the ligand binding kinetics in the presence of antagonists.


    Organizational Affiliation

    From the Departments of Biomedicine.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Integrin alpha-M
A
198Homo sapiensMutation(s): 0 
Gene Names: ITGAM (CD11B, CR3A)
Find proteins for P11215 (Homo sapiens)
Go to Gene View: ITGAM
Go to UniProtKB:  P11215
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SIM
Query on SIM

Download SDF File 
Download CCD File 
A
Simvastatin acid
DIMETHYL-COMPACTIN
C25 H40 O6
XWLXKKNPFMNSFA-HGQWONQESA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.001 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 56.380α = 90.00
b = 57.690β = 90.00
c = 58.400γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PHASERphasing
XDSdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2016-07-06
    Type: Database references
  • Version 1.2: 2016-08-24
    Type: Database references
  • Version 1.3: 2018-01-17
    Type: Data collection