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 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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 h ...

    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-13 A113Homo sapiensMutation(s): 9 
Gene Names: IL13NC30
Find proteins for P35225 (Homo sapiens)
Explore P35225 
Go to UniProtKB:  P35225
NIH Common Fund Data Resources
PHAROS:  P35225
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-4 receptor subunit alpha B203Homo sapiensMutation(s): 0 
Gene Names: IL4RIL4RA582J2.1
Find proteins for P24394 (Homo sapiens)
Explore P24394 
Go to UniProtKB:  P24394
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PHAROS:  P24394
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-13 receptor subunit alpha-1 C318Homo sapiensMutation(s): 0 
Gene Names: IL13RA1IL13RIL13RA
Find proteins for P78552 (Homo sapiens)
Explore P78552 
Go to UniProtKB:  P78552
NIH Common Fund Data Resources
PHAROS:  P78552
Protein Feature View
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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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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