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


Ligand Structure Quality Assessment 


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: https://doi.org/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. 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-13113Homo sapiensMutation(s): 9 
Gene Names: IL13NC30
UniProt & NIH Common Fund Data Resources
Find proteins for P35225 (Homo sapiens)
Explore P35225 
Go to UniProtKB:  P35225
PHAROS:  P35225
GTEx:  ENSG00000169194 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35225
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-4 receptor subunit alpha203Homo sapiensMutation(s): 0 
Gene Names: IL4RIL4RA582J2.1
UniProt & NIH Common Fund Data Resources
Find proteins for P24394 (Homo sapiens)
Explore P24394 
Go to UniProtKB:  P24394
PHAROS:  P24394
GTEx:  ENSG00000077238 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24394
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-13 receptor subunit alpha-1318Homo sapiensMutation(s): 0 
Gene Names: IL13RA1IL13RIL13RA
UniProt & NIH Common Fund Data Resources
Find proteins for P78552 (Homo sapiens)
Explore P78552 
Go to UniProtKB:  P78552
PHAROS:  P78552
GTEx:  ENSG00000131724 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP78552
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
H [auth B],
I [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
J [auth C]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
J [auth C],
K [auth C],
L [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

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



Ligand Structure Quality Assessment 


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