5E4E

Engineered Interleukin-13 bound to receptor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 

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Literature

Instructive roles for cytokine-receptor binding parameters in determining signaling and functional potency.

Moraga, I., Richter, D., Wilmes, S., Winkelmann, H., Jude, K., Thomas, C., Suhoski, M.M., Engleman, E.G., Piehler, J., Garcia, K.C.

(2015) Sci Signal 8: ra114-ra114

  • DOI: 10.1126/scisignal.aab2677
  • Primary Citation of Related Structures:  
    5E4E

  • PubMed Abstract: 

    • Cytokines dimerize cell surface receptors to activate signaling and regulate many facets of the immune response. Many cytokines have pleiotropic effects, inducing a spectrum of redundant and distinct effects on different cell types. This pleiotropy has hampered cytokine-based therapies, and the high doses required for treatment often lead to off-target effects, highlighting the need for a more detailed understanding of the parameters controlling cytokine-induced signaling and bioactivities ...

    Cytokines dimerize cell surface receptors to activate signaling and regulate many facets of the immune response. Many cytokines have pleiotropic effects, inducing a spectrum of redundant and distinct effects on different cell types. This pleiotropy has hampered cytokine-based therapies, and the high doses required for treatment often lead to off-target effects, highlighting the need for a more detailed understanding of the parameters controlling cytokine-induced signaling and bioactivities. Using the prototypical cytokine interleukin-13 (IL-13), we explored the interrelationships between receptor binding and a wide range of downstream cellular responses. We applied structure-based engineering to generate IL-13 variants that covered a spectrum of binding strengths for the receptor subunit IL-13Rα1. Engineered IL-13 variants representing a broad range of affinities for the receptor exhibited similar potencies in stimulating the phosphorylation of STAT6 (signal transducer and activator of transcription 6). Delays in the phosphorylation and nuclear translocation of STAT6 were only apparent for those IL-13 variants with markedly reduced affinities for the receptor. From these data, we developed a mechanistic model that quantitatively reproduced the kinetics of STAT6 phosphorylation for the entire spectrum of binding affinities. Receptor endocytosis played a key role in modulating STAT6 activation, whereas the lifetime of receptor-ligand complexes at the plasma membrane determined the potency of the variant for inducing more distal responses. This complex interrelationship between extracellular ligand binding and receptor function provides the foundation for new mechanism-based strategies that determine the optimal cytokine dose to enhance therapeutic efficacy.

    Organizational Affiliation: 

    Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305-5345, USA. Department of Molecular and Cellular Physiology and Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5345, USA. kcgarcia@stanford.edu piehler@uos.de.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-13A113Homo sapiensMutation(s): 9 
Gene Names: IL13, NC30
UniProt & NIH Common Fund Data Resources
Find proteins for P35225 (Homo sapiens)
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Go to UniProtKB:  P35225
PHAROS:  P35225
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UniProt GroupP35225
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-4 receptor subunit alphaB203Homo sapiensMutation(s): 0 
Gene Names: IL4R, IL4RA, 582J2.1
UniProt & NIH Common Fund Data Resources
Find proteins for P24394 (Homo sapiens)
Explore P24394 
Go to UniProtKB:  P24394
PHAROS:  P24394
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UniProt GroupP24394
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-13 receptor subunit alpha-1C318Homo sapiensMutation(s): 0 
Gene Names: IL13RA1, IL13R, IL13RA
UniProt & NIH Common Fund Data Resources
Find proteins for P78552 (Homo sapiens)
Explore P78552 
Go to UniProtKB:  P78552
PHAROS:  P78552
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UniProt GroupP78552
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 
  • Space Group: P 21 2 21
  • Diffraction Data DOI: 10.15785/SBGRID/516 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.59α = 90
b = 69.37β = 90
c = 186.8γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-02
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary