1IT9

CRYSTAL STRUCTURE OF AN ANTIGEN-BINDING FRAGMENT FROM A HUMANIZED VERSION OF THE ANTI-HUMAN FAS ANTIBODY HFE7A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Humanization of the Mouse Anti-Fas Antibody HFE7A and Crystal Structure of the Humanized HFE7A Fab Fragment

Haruyama, H.Ito, S.Miyadai, K.Takahashi, T.Kawaida, R.Takayama, T.Hanzawa, H.Hata, T.Yamaguchi, J.Yoshida-Kato, H.Ichikawa, K.Ohsumi, J.Yonehara, S.Serizawa, N.

(2002) Biol Pharm Bull 25: 1537-1545

  • DOI: 10.1248/bpb.25.1537
  • Primary Citation of Related Structures:  
    1IT9

  • PubMed Abstract: 
  • Binding of Fas ligand to Fas induces apoptosis. The Fas-Fas ligand system plays important roles in many biological processes, including the elimination of autoreactive lymphoid cells. We have previously obtained the mouse anti-Fas antibody HFE7A (m-H ...

    Binding of Fas ligand to Fas induces apoptosis. The Fas-Fas ligand system plays important roles in many biological processes, including the elimination of autoreactive lymphoid cells. We have previously obtained the mouse anti-Fas antibody HFE7A (m-HFE7A), which specifically induces apoptosis in inflammatory cells. In order to apply m-HFE7A for human therapy, we performed antibody humanization of m-HFE7A by grafting the mouse complementarity-determining regions (CDRs) to a human antibody. Five versions of humanized HFE7A (h-HFE7A) demonstrated the same antigen-binding affinity and same competition-binding activity against Fas as the chimeric HFE7A. Furthermore, these h-HFE7As induced the same degree of apoptosis in WR19L12a cells that express human Fas on their surface as chimeric HFE7A does. To further probe the structural basis for antibody humanization, we determined the three-dimensional structure of the h-HFE7A antigen-binding fragment (Fab) by X-ray crystallography and compared it with the crystal structure of the parent m-HFE7A Fab previously determined. The main-chain conformation in each h-HFE7A CDR is almost identical to that in m-HFE7A with root mean square (rms) deviations of 0.14-0.77 A. However, a significant segmental shift was observed in the CDR-L1 loop. Together with the high temperature factors of the CDR-L1 residues, both the loops are flexible, suggesting that the CDR-L1 loop would undergo conformational change upon binding to the antigen. Our results indicate that the humanization of m-HFE7A succeeded in maintaining the main-chain conformation as well as the flexibility of the CDR loop.


    Related Citations: 
    • CRYSTALLIZATION AND PRELIMINARY X-RAY STUDIES OF THE FAB FRAGMENT FROM A HUMANIZED VERSION OF THE MOUSE ANTI-HUMAN FAS ANTIBODY HFE7A
      Ito, S., Takayama, T., Hanzawa, H., Takahashi, T., Miyadai, K., Serizawa, N., Haruyama, H., Hata, T.
      () To be published --: --
    • Crystal Structure of the Antigen-Binding Fragment of Apoptosis-Inducing Mouse Anti-Human Fas Monoclonal Antibody HFE7A
      Ito, S., Takayama, T., Hanzawa, H., Ichikawa, K., Ohsumi, J., Serizawa, N., Hata, T., Haruyama, H.
      (2002) J Biochem 131: 137

    Organizational Affiliation

    Biomedical Research Laboratories, Sankyo Co, Ltd, Tokyo, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HUMANIZED ANTIBODY HFE7A, LIGHT CHAINL214Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HUMANIZED ANTIBODY HFE7A, HEAVY CHAINH219Mus musculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.365α = 90
b = 82.746β = 90
c = 104.934γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-02-25
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-12-25
    Changes: Source and taxonomy