Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 64.49 kDa 
• Atom Count: 4769 
• Modelled Residue Count: 579 
• Deposited Residue Count: 588 
• Unique protein chains: 3

4G6J

Crystal structure of human IL-1beta in complex with the therapeutic antibody binding fragment of canakinumab

• PDB DOI: 10.2210/pdb4G6J/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2012-07-19 Released: 2012-12-19 
• Deposition Author(s): Blech, M., Hoerer, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.252 
• R-Value Work: 0.226 
• R-Value Observed: 0.227 

Literature

One traget-two different binding modes: Structural insights into gevokizumab and canakinumab interactions to interleukin-1beta

Blech, M., Peter, D., Fischer, P., Bauer, M.M., Hafner, M., Zeeb, M., Nar, H.

(2013) J Mol Biol 425: 94-111

• PubMed: 23041424 
• DOI: 10.1016/j.jmb.2012.09.021
• Primary Citation of Related Structures:  
  4G5Z, 4G6J, 4G6K, 4G6M


• PubMed Abstract: 
  

Interleukin-1β (IL-1β) is a key orchestrator in inflammatory and several immune responses. IL-1β exerts its effects through interleukin-1 receptor type I (IL-1RI) and interleukin-1 receptor accessory protein (IL-1RAcP), which together form a heterotrimeric signaling-competent complex. Canakinumab and gevokizumab are highly specific IL-1β monoclonal antibodies. Canakinumab is known to neutralize IL-1β by competing for binding to IL-1R and therefore blocking signaling by the antigen:antibody complex. Gevokizumab is claimed to be a regulatory therapeutic antibody that modulates IL-1β bioactivity by reducing the affinity for its IL-1RI:IL-1RAcP signaling complex. How IL-1β signaling is affected by both canakinumab and gevokizumab was not yet experimentally determined. We have analyzed the crystal structures of canakinumab and gevokizumab antibody binding fragment (Fab) as well as of their binary complexes with IL-1β. Furthermore, we characterized the epitopes on IL-1β employed by the antibodies by NMR epitope mapping studies. The direct comparison of NMR and X-ray data shows that the epitope defined by the crystal structure encompasses predominantly those residues whose NMR resonances are severely perturbed upon complex formation. The antigen:Fab co-structures confirm the previously identified key contact residues on IL-1β and provide insight into the mechanisms leading to their distinct modulation of IL-1β signaling. A significant steric overlap of the binding interfaces of IL-1R and canakinumab on IL-1β causes competitive inhibition of the association of IL-1β and its receptor. In contrast, gevokizumab occupies an allosteric site on IL-1β and complex formation results in a minor reduction of binding affinity to IL-1RI. This suggests two different mechanisms of IL-1β pathway attenuation.

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Organizational Affiliation: 

Department of Lead Identification and Optimization Support, Structural Research Group, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88397 Biberach, Germany. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-1 beta	A	158	Homo sapiens	Mutation(s): 0  Gene Names: IL1B, IL1F2
UniProt & NIH Common Fund Data Resources
Find proteins for P01584 (Homo sapiens) Explore P01584  Go to UniProtKB:  P01584
PHAROS:  P01584

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
heavy chain of antibody binding fragment of canakinumab	B [auth H]	218	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
light chain of antibody binding fragment of canakinumab	C [auth L]	212	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.252 
• R-Value Work: 0.226 
• R-Value Observed: 0.227 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.061	α = 90
b = 37.3	β = 90
c = 189.418	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
AutoPROC	data collection
PHASER	phasing
BUSTER	refinement
XDS	data reduction
AutoPROC	data scaling
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-07-19 
• Released Date: 2012-12-19 
Deposition Author(s): Blech, M., Hoerer, S.

Revision History  

• Version 1.0: 2012-12-19
  Type: Initial release
  
• Version 1.1: 2013-07-17
  Changes: Database references