7CHZ

Crystal Structure Of Human Il-1beta In Complex With Antibody Binding Fragment Of IgG26A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.193 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure-based Development of Human Interleukin-1 beta-Specific Antibody That Simultaneously Inhibits Binding to Both IL-1RI and IL-1RAcP.

Kuo, W.C.Lee, C.C.Chang, Y.W.Pang, W.Chen, H.S.Hou, S.C.Lo, S.Y.Yang, A.S.Wang, A.H.

(2020) J Mol Biol 433: 166766-166766

  • DOI: https://doi.org/10.1016/j.jmb.2020.166766
  • Primary Citation of Related Structures:  
    7CHY, 7CHZ

  • PubMed Abstract: 

    Interleukin-1β (IL-1β) is a potent pleiotropic cytokine playing a central role in protecting cells from microbial pathogen infection or endogenous stress. After it binds to IL-1RI and recruits IL-1 receptor accessory protein (IL-1RAcP), signaling culminates in activation of NF-κB. Many pathophysiological diseases have been attributed to the derailment of IL-1β regulation. Several blocking reagents have been developed based on two mechanisms: blocking the binding of IL-1β to IL-1RI or inhibiting the recruitment of IL-1RAcP to the IL-1β initial complex. In order to simultaneously fulfill these two actions, a human anti-IL-1β neutralizing antibody IgG26 was screened from human genetic phage-display library and furthered structure-optimized to final version, IgG26AW. IgG26AW has a sub-nanomolar binding affinity for human IL-1β. We validated IgG26AW-neutralizing antibodies specific for IL-1β in vivo to prevent human IL-1β-driving IL-6 elevation in C56BL/6 mice. Mice underwent treatments with IgG26AW in A549 and MDA-MB-231 xenograft mouse cancer models have also been observed with tumor shrank and inhibition of tumor metastasis. The region where IgG26 binds to IL-1β also overlaps with the position where IL-1RI and IL-1RAcP bind, as revealed by the 26-Fab/IL-1β complex structure. Meanwhile, SPR experiments showed that IL-1β bound by IgG26AW prevented the further binding of IL-1RI and IL-1RAcP, which confirmed our inference from the result of protein structure. Therefore, the inhibitory mechanism of IgG26AW is to block the assembly of the IL-1β/IL-1RI/IL-1RAcP ternary complex which further inhibits downstream signaling. Based on its high affinity, high neutralizing potency, and novel binding epitope simultaneously occupying both IL-1RI and IL-1RAcP residues that bind to IL-1β, IgG26AW may be a new candidate for treatments of inflammation-related diseases or for complementary treatments of cancers in which the role of IL-1β is critical to pathogenesis.


  • Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
light chain of antibody binding fragment of IgG26AA [auth L]214Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
heavy chain of antibody binding fragment of IgG26AB [auth H]227Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-1 betaC [auth I]157Homo sapiensMutation(s): 0 
Gene Names: IL1BIL1F2
UniProt & NIH Common Fund Data Resources
Find proteins for P01584 (Homo sapiens)
Explore P01584 
Go to UniProtKB:  P01584
PHAROS:  P01584
GTEx:  ENSG00000125538 
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UniProt GroupP01584
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.193 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.694α = 90
b = 112.699β = 94.531
c = 38.935γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-13
    Type: Initial release
  • Version 1.1: 2021-01-27
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary