Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 73.36 kDa 
• Atom Count: 4723 
• Residue Count: 597 
• Unique protein chains: 3

5E4E

Engineered Interleukin-13 bound to receptor

• DOI: 10.2210/pdb5E4E/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2015-10-05 Released: 2015-12-02 
• Deposition Author(s): Moraga, I., Thomas, C., Jude, K.M., Garcia, K.C.

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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 

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

• PubMed: 26554818 
• 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. 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.

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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. [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-13	A	113	Homo sapiens	Mutation(s): 9  Gene Names: IL13, NC30
Find proteins for P35225 (Homo sapiens) Explore P35225  Go to UniProtKB:  P35225
NIH Common Fund Data Resources
PHAROS:  P35225 GTEx:  ENSG00000169194

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-4 receptor subunit alpha	B	203	Homo sapiens	Mutation(s): 0  Gene Names: IL4R, IL4RA, 582J2.1
Find proteins for P24394 (Homo sapiens) Explore P24394  Go to UniProtKB:  P24394
NIH Common Fund Data Resources
PHAROS:  P24394 GTEx:  ENSG00000077238

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-13 receptor subunit alpha-1	C	318	Homo sapiens	Mutation(s): 0  Gene Names: IL13RA1, IL13R, IL13RA
Find proteins for P78552 (Homo sapiens) Explore P78552  Go to UniProtKB:  P78552
NIH Common Fund Data Resources
PHAROS:  P78552 GTEx:  ENSG00000131724

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	A, C	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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 = 62.59	α = 90
b = 69.37	β = 90
c = 186.8	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-10-05 
• Released Date: 2015-12-02 
Deposition Author(s): Moraga, I., Thomas, C., Jude, K.M., Garcia, K.C.

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