5BVJ | pdb_00005bvj

The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1beta


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.228 (Depositor) 
  • R-Value Work: 
    0.186 (Depositor), 0.193 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5BVJ

This is version 2.1 of the entry. See complete history

Literature

The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1 beta.

Rondeau, J.M.Ramage, P.Zurini, M.Gram, H.

(2015) MAbs 7: 1151-1160

  • DOI: https://doi.org/10.1080/19420862.2015.1081323
  • Primary Citation Related Structures: 
    5BVJ, 5BVP

  • PubMed Abstract: 

    Interleukin-1β (IL-1β) plays a key role in autoinflammatory diseases, such as systemic juvenile idiopathic arthritis (sJIA) or cryopyrin-associated periodic syndrome (CAPS). Canakinumab, a human monoclonal anti-IL-1β antibody, was recently approved for human use under the brand name Ilaris®. Canakinumab does not cross-react with IL-1β from mouse, rat, rabbit, or macaques. The crystal structure of the canakinumab Fab bound to human IL-1β was determined in an attempt to rationalize the species specificity. The X-ray analysis reveals a complex surface epitope with an intricate network of well-ordered water molecules at the antibody-antigen interface. The canakinumab paratope is largely pre-organized, as demonstrated by the structure determination of the free Fab. Glu 64 of human IL-1β is a pivotal epitope residue explaining the exquisite species specificity of canakinumab. We identified marmoset as the only non-human primate species that carries Glu 64 in its IL-1β and demonstrates full cross-reactivity of canakinumab, thereby enabling toxicological studies in this species. As demonstrated by the X-ray structure of the complex with IL-1β, canakinumab binds IL-1β on the opposite side with respect to the IL-1RAcP binding site, and in an approximately orthogonal orientation with respect to IL-1RI. However, the antibody and IL-1RI binding sites slightly overlap and the VH region of canakinumab would sterically interfere with the D1 domain of IL-1RI, as shown by a structural overlay with the IL-1β:IL-1RI complex. Therefore, direct competition with IL-1RI for IL-1β binding is the molecular mechanism of neutralization by canakinumab, which is also confirmed by competition assays with recombinant IL-1RI and IL-1RII.


  • Organizational Affiliation
    • a Novartis Institutes for BioMedical Research ; Basel , Switzerland.

Macromolecule Content 

  • Total Structure Weight: 190.24 kDa 
  • Atom Count: 14,437 
  • Modeled Residue Count: 1,732 
  • Deposited Residue Count: 1,756 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
canakinumab Fab light-chain
A, C, E, G
214Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
canakinumab Fab heavy-chain
B, D, F, H
225Homo sapiensMutation(s): 0 

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
B, D, F, H
L-PEPTIDE LINKINGC5 H7 N O3GLN

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.228 (Depositor) 
  • R-Value Work:  0.186 (Depositor), 0.193 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.621α = 90
b = 142.264β = 115.76
c = 83.802γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-02
    Type: Initial release
  • Version 1.1: 2015-09-30
    Changes: Database references
  • Version 1.2: 2015-10-28
    Changes: Database references
  • Version 2.0: 2020-03-11
    Changes: Atomic model, Data collection, Polymer sequence
  • Version 2.1: 2024-11-13
    Changes: Data collection, Database references, Structure summary