4GAF

Crystal structure of EBI-005, a chimera of human IL-1beta and IL-1Ra, bound to human Interleukin-1 receptor type 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.271 (Depositor), 0.281 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

Design of a superior cytokine antagonist for topical ophthalmic use.

Hou, J.Townson, S.A.Kovalchin, J.T.Masci, A.Kiner, O.Shu, Y.King, B.M.Schirmer, E.Golden, K.Thomas, C.Garcia, K.C.Zarbis-Papastoitsis, G.Furfine, E.S.Barnes, T.M.

(2013) Proc Natl Acad Sci U S A 110: 3913-3918

  • DOI: https://doi.org/10.1073/pnas.1217996110
  • Primary Citation of Related Structures:  
    4GAF, 4GAI

  • PubMed Abstract: 

    IL-1 is a key inflammatory and immune mediator in many diseases, including dry-eye disease, and its inhibition is clinically efficacious in rheumatoid arthritis and cryopyrin-associated periodic syndromes. To treat ocular surface disease with a topical biotherapeutic, the uniqueness of the site necessitates consideration of the agent's size, target location, binding kinetics, and thermal stability. Here we chimerized two IL-1 receptor ligands, IL-1β and IL-1Ra, to create an optimized receptor antagonist, EBI-005, for topical ocular administration. EBI-005 binds its target, IL-1R1, 85-fold more tightly than IL-1Ra, and this increase translates to an ∼100-fold increase in potency in vivo. EBI-005 preserves the affinity bias of IL-1Ra for IL-1R1 over the decoy receptor (IL-1R2), and, surprisingly, is also more thermally stable than either parental molecule. This rationally designed antagonist represents a unique approach to therapeutic design that can potentially be exploited for other β-trefoil family proteins in the IL-1 and FGF families.


  • Organizational Affiliation

    Eleven Biotherapeutics, Inc., Cambridge, MA 02142, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EBI-005153Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01584 (Homo sapiens)
Explore P01584 
Go to UniProtKB:  P01584
PHAROS:  P01584
GTEx:  ENSG00000125538 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01584
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-1 receptor type 1319Homo sapiensMutation(s): 0 
Gene Names: IL1R1IL1RIL1RAIL1RT1
EC: 3.2.2.6
UniProt & NIH Common Fund Data Resources
Find proteins for P14778 (Homo sapiens)
Explore P14778 
Go to UniProtKB:  P14778
PHAROS:  P14778
GTEx:  ENSG00000115594 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14778
Glycosylation
Glycosylation Sites: 4Go to GlyGen: P14778-1
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.271 (Depositor), 0.281 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.35α = 90
b = 149.27β = 90
c = 126.17γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-20
    Type: Initial release
  • Version 1.1: 2013-03-27
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2024-10-16
    Changes: Data collection, Database references, Structure summary