3VA2 | pdb_00003va2

Crystal structure of human Interleukin-5 in complex with its alpha receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.276 (Depositor), 0.276 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3VA2

This is version 1.1 of the entry. See complete history

Literature

Structural basis of interleukin-5 dimer recognition by its alpha receptor

Kusano, S.Kukimoto-Niino, M.Hino, N.Ohsawa, N.Ikutani, M.Takaki, S.Sakamoto, K.Hara-Yokoyama, M.Shirouzu, M.Takatsu, K.Yokoyama, S.

(2012) Protein Sci 21: 850-864

  • DOI: https://doi.org/10.1002/pro.2072
  • Primary Citation Related Structures: 
    3VA2

  • PubMed Abstract: 

    Interleukin-5 (IL-5), a major hematopoietin, stimulates eosinophil proliferation, migration, and activation, which have been implicated in the pathogenesis of allergic inflammatory diseases, such as asthma. The specific IL-5 receptor (IL-5R) consists of the IL-5 receptor α subunit (IL-5RA) and the common receptor β subunit (βc). IL-5 binding to IL-5R on target cells induces rapid tyrosine phosphorylation and activation of various cellular proteins, including JAK1/JAK2 and STAT1/STAT5. Here, we report the crystal structure of dimeric IL-5 in complex with the IL-5RA extracellular domains. The structure revealed that IL-5RA sandwiches the IL-5 homodimer by three tandem domains, arranged in a "wrench-like" architecture. This association mode was confirmed for human cells expressing IL-5 and the full-length IL-5RA by applying expanded genetic code technology: protein photo-cross-linking experiments revealed that the two proteins interact with each other in vivo in the same manner as that in the crystal structure. Furthermore, a comparison with the previously reported, partial GM-CSF•GM-CSFRA•βc structure enabled us to propose complete structural models for the IL-5 and GM-CSF receptor complexes, and to identify the residues conferring the cytokine-specificities of IL-5RA and GM-CSFRA.


  • Organizational Affiliation
    • RIKEN Systems and Structural Biology Center, Tsurumi-ku, Yokohama, Japan.

Macromolecule Content 

  • Total Structure Weight: 63.14 kDa 
  • Atom Count: 4,235 
  • Modeled Residue Count: 523 
  • Deposited Residue Count: 560 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Interleukin-5
A, B
119Homo sapiensMutation(s): 0 
Gene Names: IL5
UniProt & NIH Common Fund Data Resources
Find proteins for P05113 (Homo sapiens)
Explore P05113 
Go to UniProtKB:  P05113
PHAROS:  P05113
GTEx:  ENSG00000113525 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05113
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Interleukin-5 receptor subunit alpha322Homo sapiensMutation(s): 0 
Gene Names: IL5RAIL5R
UniProt & NIH Common Fund Data Resources
Find proteins for Q01344 (Homo sapiens)
Explore Q01344 
Go to UniProtKB:  Q01344
PHAROS:  Q01344
GTEx:  ENSG00000091181 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01344
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.276 (Depositor), 0.276 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.633α = 90
b = 88.68β = 90
c = 126.674γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SOLVEphasing
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-25
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Data collection, Database references, Structure summary