4GAF

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

• PDB DOI:  https://doi.org/10.2210/pdb4GAF/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-07-25 Released: 2013-02-20 
• Deposition Author(s): Hou, J., Townson, S.A., Kovalchin, J.T., Masci, A., Kiner, O., Shu, Y., King, B., Thomas, C., Garcia, K.C., Furfine, E.S., Barnes, T.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.271 
• R-Value Work: 0.215 
• R-Value Observed: 0.218 

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

• PubMed: 23431173 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 55.37 kDa 
• Atom Count: 4,001 
• Modelled Residue Count: 458 
• Deposited Residue Count: 472 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EBI-005	A	153	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
Interleukin-1 receptor type 1	B	319	Homo sapiens	Mutation(s): 0  Gene Names: IL1R1, IL1R, IL1RA, IL1RT1 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth B], D [auth B], E [auth B], F [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
NA	G [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.271 
• R-Value Work: 0.215 
• R-Value Observed: 0.218 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.35	α = 90
b = 149.27	β = 90
c = 126.17	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-20 
Deposition Author(s): Hou, J., Townson, S.A., Kovalchin, J.T., Masci, A., Kiner, O., Shu, Y., King, B., Thomas, C., Garcia, K.C., Furfine, E.S., Barnes, T.M.

Revision History  

• 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