8UPB | pdb_00008upb

De novo designed IL-6 mimetic

• PDB DOI: https://doi.org/10.2210/pdb8UPB/pdb

• Classification: CYTOKINE
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2023-10-22 Released: 2024-08-28 
• Deposition Author(s): Borowska, M.T., Jude, K.M., Garcia, K.C.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), The Mark Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 
  0.229 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: in silico

Literature

De novo design of miniprotein antagonists of cytokine storm inducers.

Huang, B., Coventry, B., Borowska, M.T., Arhontoulis, D.C., Exposit, M., Abedi, M., Jude, K.M., Halabiya, S.F., Allen, A., Cordray, C., Goreshnik, I., Ahlrichs, M., Chan, S., Tunggal, H., DeWitt, M., Hyams, N., Carter, L., Stewart, L., Fuller, D.H., Mei, Y., Garcia, K.C., Baker, D.

(2024) Nat Commun 15: 7064-7064

• PubMed: 39152100 
• DOI: https://doi.org/10.1038/s41467-024-50919-4
• Primary Citation Related Structures: 
  8UOS, 8UPA, 8UPB


• PubMed Abstract: 
  

  Cytokine release syndrome (CRS), commonly known as cytokine storm, is an acute systemic inflammatory response that is a significant global health threat. Interleukin-6 (IL-6) and interleukin-1 (IL-1) are key pro-inflammatory cytokines involved in CRS and are hence critical therapeutic targets. Current antagonists, such as tocilizumab and anakinra, target IL-6R/IL-1R but have limitations due to their long half-life and systemic anti-inflammatory effects, making them less suitable for acute or localized treatments. Here we present the de novo design of small protein antagonists that prevent IL-1 and IL-6 from interacting with their receptors to activate signaling. The designed proteins bind to the IL-6R, GP130 (an IL-6 co-receptor), and IL-1R1 receptor subunits with binding affinities in the picomolar to low-nanomolar range. X-ray crystallography studies reveal that the structures of these antagonists closely match their computational design models. In a human cardiac organoid disease model, the IL-1R antagonists demonstrated protective effects against inflammation and cardiac damage induced by IL-1β. These minibinders show promise for administration via subcutaneous injection or intranasal/inhaled routes to mitigate acute cytokine storm effects.

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Organizational Affiliation: 
• Department of Biochemistry, University of Washington, Seattle, WA, USA.
Institute for Protein Design, University of Washington, Seattle, WA, USA.
Department of Bioengineering, University of Washington, Seattle, WA, USA.
Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
Molecular and Cellular Biology and Pathobiology Program, Medical University of South Carolina, Charleston, SC, USA.
Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
Department of Microbiology, University of Washington, Seattle, WA, USA.
Department of Bioengineering, Clemson University, Charleston, SC, USA.
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
Department of Biochemistry, University of Washington, Seattle, WA, USA. [e-mail].
Department of Bioengineering, University of Washington, Seattle, WA, USA. [e-mail].
Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 7.83 kDa 
• Atom Count: 641 
• Modeled Residue Count: 64 
• Deposited Residue Count: 64 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
De novo designed IL-6 mimetic	A	64	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free:  0.229 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.01	α = 90
b = 47.01	β = 90
c = 74.207	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-08-28 
Deposition Author(s): Borowska, M.T., Jude, K.M., Garcia, K.C.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	RO1-AI51321
The Mark Foundation	United States	--

Revision History  

• Version 1.0: 2024-08-28
  Type: Initial release