5E4E

Engineered Interleukin-13 bound to receptor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.0 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

  • 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 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Interleukin-13
A
113Homo sapiensMutation(s): 9 
Gene Names: IL13 (NC30)
Find proteins for P35225 (Homo sapiens)
Go to Gene View: IL13
Go to UniProtKB:  P35225
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Interleukin-4 receptor subunit alpha
B
203Homo sapiensMutation(s): 0 
Gene Names: IL4R (IL4RA)
Find proteins for P24394 (Homo sapiens)
Go to Gene View: IL4R
Go to UniProtKB:  P24394
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Interleukin-13 receptor subunit alpha-1
C
318Homo sapiensMutation(s): 0 
Gene Names: IL13RA1 (IL13R, IL13RA)
Find proteins for P78552 (Homo sapiens)
Go to Gene View: IL13RA1
Go to UniProtKB:  P78552
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 62.590α = 90.00
b = 69.370β = 90.00
c = 186.800γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-02
    Type: Initial release