6DG6

Structure of a de novo designed Interleukin-2/Interleukin-15 mimetic


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

De novo design of potent and selective mimics of IL-2 and IL-15.

Silva, D.A.Yu, S.Ulge, U.Y.Spangler, J.B.Jude, K.M.Labao-Almeida, C.Ali, L.R.Quijano-Rubio, A.Ruterbusch, M.Leung, I.Biary, T.Crowley, S.J.Marcos, E.Walkey, C.D.Weitzner, B.D.Pardo-Avila, F.Castellanos, J.Carter, L.Stewart, L.Riddell, S.R.Pepper, M.Bernardes, G.J.L.Dougan, M.Garcia, K.C.Baker, D.

(2019) Nature 565: 186-191

  • DOI: https://doi.org/10.1038/s41586-018-0830-7
  • Primary Citation of Related Structures:  
    6DG6

  • PubMed Abstract: 

    We describe a de novo computational approach for designing proteins that recapitulate the binding sites of natural cytokines, but are otherwise unrelated in topology or amino acid sequence. We use this strategy to design mimics of the central immune cytokine interleukin-2 (IL-2) that bind to the IL-2 receptor βγ c heterodimer (IL-2Rβγ c ) but have no binding site for IL-2Rα (also called CD25) or IL-15Rα (also known as CD215). The designs are hyper-stable, bind human and mouse IL-2Rβγ c with higher affinity than the natural cytokines, and elicit downstream cell signalling independently of IL-2Rα and IL-15Rα. Crystal structures of the optimized design neoleukin-2/15 (Neo-2/15), both alone and in complex with IL-2Rβγ c , are very similar to the designed model. Neo-2/15 has superior therapeutic activity to IL-2 in mouse models of melanoma and colon cancer, with reduced toxicity and undetectable immunogenicity. Our strategy for building hyper-stable de novo mimetics could be applied generally to signalling proteins, enabling the creation of superior therapeutic candidates.


  • Organizational Affiliation

    Institute for Protein Design, University of Washington, Seattle, WA, USA. dadriano@uw.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neoleukin-2/15
A, B, C, D, E
A, B, C, D, E, F
104synthetic 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 = 73.73α = 90
b = 86.8β = 90
c = 92.31γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

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 StatesRO1-AI51321

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-16
    Type: Initial release
  • Version 1.1: 2019-01-23
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references
  • Version 1.4: 2024-04-03
    Changes: Refinement description