3LB6

The structure of IL-13 in complex with IL-13Ralpha2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular basis for shared cytokine recognition revealed in the structure of an unusually high affinity complex between IL-13 and IL-13Ralpha2.

Lupardus, P.J.Birnbaum, M.E.Garcia, K.C.

(2010) Structure 18: 332-342

  • DOI: 10.1016/j.str.2010.01.003
  • Primary Citation of Related Structures:  
    3LB6

  • PubMed Abstract: 
  • Interleukin-13 is a cytokine important for development of T helper cell type 2 (Th2) responses and plays a critical role in asthma and allergy. The IL-13 Receptor alpha2 (IL-13Ralpha2) is a receptor for IL-13 lacking canonical Jak/STAT signaling functions ...

    Interleukin-13 is a cytokine important for development of T helper cell type 2 (Th2) responses and plays a critical role in asthma and allergy. The IL-13 Receptor alpha2 (IL-13Ralpha2) is a receptor for IL-13 lacking canonical Jak/STAT signaling functions. Here we present the crystal structure along with a mutational and biophysical analysis of the IL-13/IL-13Ralpha2 complex. While retaining a similar mode of IL-13 binding to its related signaling receptor, IL-13Ralpha1, IL-13Ralpha2 uses peripheral receptor residues unused in the IL-13/IL-13Ralpha1 complex to generate a larger and more complementary interface for IL-13. This results in a four orders of magnitude increase in affinity, to the femtomolar level, compared to IL-13Ralpha1. Alanine scanning mutagenesis of the IL-13 interface reveals several common "hotspot" residues important for binding to both receptors, but also identifies a prominent IL-13Ralpha2-specific contact. These results provide a framework for development of receptor subtype-selective IL-13 antagonists and indicate a decoy function for IL-13Ralpha2.


    Organizational Affiliation

    Howard Hughes Medical Institute, Department of Molecular and Cellular Physiology, Department of Structural Biology, and Program in Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-13A132Homo sapiensMutation(s): 0 
Gene Names: IL13NC30
Find proteins for P35225 (Homo sapiens)
Explore P35225 
Go to UniProtKB:  P35225
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PHAROS:  P35225
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-13 receptor subunit alpha-2B [auth C]380Homo sapiensMutation(s): 1 
Gene Names: IL13RA2IL13R
Find proteins for Q14627 (Homo sapiens)
Explore Q14627 
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PHAROS:  Q14627
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-13C [auth B]132Homo sapiensMutation(s): 0 
Gene Names: IL13NC30
Find proteins for P35225 (Homo sapiens)
Explore P35225 
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PHAROS:  P35225
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-13 receptor subunit alpha-2D380Homo sapiensMutation(s): 1 
Gene Names: IL13RA2IL13R
Find proteins for Q14627 (Homo sapiens)
Explore Q14627 
Go to UniProtKB:  Q14627
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PHAROS:  Q14627
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth C], G [auth D]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth C], H [auth D]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLY
Query on MLY
B [auth C]L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.37α = 90
b = 86.57β = 96.77
c = 166.788γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary