Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 73361.30 
• Atom Count: 4723 
• Residue Count: 634 
• 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): 9 


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

---

Experimental Data Snapshot

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

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


• 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: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Interleukin-13	A	113	Homo sapiens	Mutation(s): 9  Gene Names: IL13 (NC30)
Find proteins for P35225 (Homo sapiens) Go to Gene View: IL13 Go to UniProtKB:  P35225

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Interleukin-4 receptor subunit alpha	B	203	Homo sapiens	Mutation(s): 0  Gene Names: IL4R (IL4RA)
Find proteins for P24394 (Homo sapiens) Go to Gene View: IL4R Go to UniProtKB:  P24394

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Interleukin-13 receptor subunit alpha-1	C	318	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A, C	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NAG	B	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3 Å
• R-Value Free: 0.288 
• R-Value Work: 0.234 
• Space Group: P 2₁ 2 2₁
• Diffraction Data DOI: 
  10.15785/SBGRID/516 SBGrid

Unit Cell:

Length (Å)	Angle (°)
a = 62.590	α = 90.00
b = 69.370	β = 90.00
c = 186.800	γ = 90.00

Software Package:

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

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