4HWE | pdb_00004hwe

Crystal structure of ectodomain 3 of the IL-13 receptor alpha1 in complex with a human neutralizing monoclonal antibody fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 
    0.223 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4HWE

This is version 1.2 of the entry. See complete history

Literature

Crystal structure of ectodomain 3 of the IL-13 receptor alpha1 in complex with a human neutralizing monoclonal antibody fragment

Redpath, N.T.Xu, Y.Wilson, N.J.Fabri, L.J.Baca, M.Andrews, A.E.Braley, H.Lu, P.Ireland, C.Ernst, R.E.Woods, A.Forrest, G.An, Z.Zaller, D.M.Strohl, W.R.Luo, C.S.Czabotar, P.E.Garrett, T.P.Hilton, D.J.Nash, A.D.Zhang, J.G.Nicola, N.A.

(2013) Biochem J 451: 165-175

  • DOI: https://doi.org/10.1042/BJ20121819
  • Primary Citation Related Structures: 
    4HWB, 4HWE

  • PubMed Abstract: 

    Gene deletion studies in mice have revealed critical roles for IL (interleukin)-4 and -13 in asthma development, with the latter controlling lung airways resistance and mucus secretion. We have now developed human neutralizing monoclonal antibodies against human IL-13Rα1 (IL-13 receptor α1) subunit that prevent activation of the receptor complex by both IL-4 and IL-13. We describe the crystal structures of the Fab fragment of antibody 10G5H6 alone and in complex with D3 (ectodomain 3) of IL-13Rα1. Although the structure showed significant domain swapping within a D3 dimer, we showed that Arg(230), Phe(233), Tyr(250), Gln(252) and Leu(293) in each D3 monomer and Ser(32), Asn(102) and Trp(103) in 10G5H6 Fab are the key interacting residues at the interface of the 10G5H6 Fab-D3 complex. One of the most striking contacts is the insertion of the ligand-contacting residue Leu(293) of D3 into a deep pocket on the surface of 10G5H6 Fab, and this appears to be a central determinant of the high binding affinity and neutralizing activity of the antibody.


  • Organizational Affiliation
    • The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.

Macromolecule Content 

  • Total Structure Weight: 48.71 kDa 
  • Atom Count: 3,531 
  • Modeled Residue Count: 423 
  • Deposited Residue Count: 438 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab heavy chainA [auth H]227Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab light chainB [auth L]211Homo sapiensMutation(s): 0 

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth H],
D [auth H],
E [auth H],
L
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
F [auth H]
G [auth H]
H
I [auth H]
J [auth H]
F [auth H],
G [auth H],
H,
I [auth H],
J [auth H],
K [auth H],
M [auth L],
N [auth L],
O [auth L],
P [auth L]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free:  0.223 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.364α = 90
b = 121.364β = 90
c = 152.107γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASERphasing
BUSTERrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2013-02-27 
  • Deposition Author(s): Xu, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2013-07-24
    Changes: Database references
  • Version 1.2: 2024-11-27
    Changes: Data collection, Database references, Derived calculations, Structure summary