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CRYSTAL STRUCTURE OF THE FAB FRAGMENT OF THE MOUSE ANTI-HUMAN FAS ANTIBODY HFE7A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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.(Tokyo) 131: 137-143


  • 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. The mouse anti-human Fas monoclonal antibody HFE7A (m-HFE7A), whic ...

    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. The mouse anti-human Fas monoclonal antibody HFE7A (m-HFE7A), which induces apoptosis, has been humanized based on a structure predicted by homology modeling. A version of humanized HFE7A is currently under development for the treatment of autoimmune diseases such as rheumatoid arthritis. For a deeper understanding of the protein engineering aspect of antibody humanization, for which information on the three-dimensional structure is essential, we determined the crystal structure of the m-HFE7A antigen-binding fragment (Fab) by X-ray crystallography at 2.5 A resolution. The main-chain conformation of the five loops in the six complementarity-determining regions (CDRs) was correctly predicted with root-mean-square deviations of 0.30-1.04 A based on a comparison of the crystal structure with the predicted structure. The CDR-H3 conformation of the crystal structure, which was not classified as one of the canonical structures, was completely different from that of the predicted structure but adopted the conformation which followed the "H3-rules." The results of charge distribution analysis of the antigen-binding site suggest that electrostatic interactions may be important for its binding to Fas.


    Related Citations: 
    • Cloning and expression of a novel murine anti-human Fas antibody
      Yoshida-Kato, H.,Ichikawa, K.,Yamaguchi, J.,Watanabe, K.,Ohsumi, J.,Yonehara, S.,Serizawa, N.
      (2000) BIOSCI.BIOTECHNOL.BIOCHEM. 64: 1903
    • A novel murine anti-human Fas mAb which mitigates lymphadenopathy without hepatotoxicity
      Ichikawa, K.,Yoshida-Kato, H.,Ohtsuki, M.,Ohsumi, J.,Yamaguchi, J.,Takahashi, S.,Tani, Y.,Watanabe, M.,Shiraishi, A.,Nishioka, K.,Yonehara, S.,Serizawa, N.
      (2000) INT.IMMUNOL. 12: 555
    • Crystallization and preliminary X-ray crystallographic studies on a Fab fragment of the mouse anti-human Fas monoclonal antibody HFE7A
      Ito, S.,Takayama, T.,Hanzawa, H.,Ichikawa, K.,Ohsumi, J.,Serizawa, N.,Haruyama, H.,Hata, T.
      (2001) Acta Crystallogr.,Sect.D 57: 1700


    Organizational Affiliation

    Biomedical Research Laboratories, Sankyo Co., Ltd., 140-8710, Japan. shuici@shina.sankyo.co.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ANTIBODY M-HFE7A, LIGHT CHAIN
L
218N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ANTIBODY M-HFE7A, HEAVY CHAIN
H
230N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 43.435α = 90.00
b = 73.965β = 90.00
c = 133.773γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
SCALEPACKdata scaling
X-PLORmodel building
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-01-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-06-20
    Type: Data collection, Database references, Structure summary