8DZ8

Neoleukin 4, a de novo designed IL-4 mimetic


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Design of cell-type-specific hyperstable IL-4 mimetics via modular de novo scaffolds.

Yang, H.Ulge, U.Y.Quijano-Rubio, A.Bernstein, Z.J.Maestas, D.R.Chun, J.H.Wang, W.Lin, J.X.Jude, K.M.Singh, S.Orcutt-Jahns, B.T.Li, P.Mou, J.Chung, L.Kuo, Y.H.Ali, Y.H.Meyer, A.S.Grayson, W.L.Heller, N.M.Garcia, K.C.Leonard, W.J.Silva, D.A.Elisseeff, J.H.Baker, D.Spangler, J.B.

(2023) Nat Chem Biol 19: 1127-1137

  • DOI: https://doi.org/10.1038/s41589-023-01313-6
  • Primary Citation of Related Structures:  
    8DZ8

  • PubMed Abstract: 

    The interleukin-4 (IL-4) cytokine plays a critical role in modulating immune homeostasis. Although there is great interest in harnessing this cytokine as a therapeutic in natural or engineered formats, the clinical potential of native IL-4 is limited by its instability and pleiotropic actions. Here, we design IL-4 cytokine mimetics (denoted Neo-4) based on a de novo engineered IL-2 mimetic scaffold and demonstrate that these cytokines can recapitulate physiological functions of IL-4 in cellular and animal models. In contrast with natural IL-4, Neo-4 is hyperstable and signals exclusively through the type I IL-4 receptor complex, providing previously inaccessible insights into differential IL-4 signaling through type I versus type II receptors. Because of their hyperstability, our computationally designed mimetics can directly incorporate into sophisticated biomaterials that require heat processing, such as three-dimensional-printed scaffolds. Neo-4 should be broadly useful for interrogating IL-4 biology, and the design workflow will inform targeted cytokine therapeutic development.


  • Organizational Affiliation

    Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
neoleukin-4
A, B, C, D, E
A, B, C, D, E, F, G, H
101synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.477α = 90
b = 122.477β = 90
c = 310.376γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
BUSTERrefinement
XSCALEdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI051321

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-29
    Type: Initial release
  • Version 1.1: 2023-04-26
    Changes: Database references
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references
  • Version 1.3: 2023-10-25
    Changes: Refinement description