2GJJ

Crystal structure of a single chain antibody scA21 against Her2/ErbB2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Epitope mapping and structural analysis of an anti-ErbB2 antibody A21: Molecular basis for tumor inhibitory mechanism

Hu, S.Zhu, Z.Li, L.Chang, L.Li, W.Cheng, L.Teng, M.Liu, J.

(2007) Proteins 70: 938-949

  • DOI: https://doi.org/10.1002/prot.21551
  • Primary Citation of Related Structures:  
    2GJJ

  • PubMed Abstract: 

    Anti-ErbB2 antibodies targeting distinct epitopes can have different biological functions on cancer cells. A21 prepared by surface epitope masking (SEM) method is a tumor-inhibitory anti-ErbB2 monoclonal antibody. Previously we engineered a single chain chimeric antibody chA21 with potential for therapy of ErbB2-overexpressing tumors. Here, we mapped the A21 epitope on ErbB2 extracellular domain (ECD) by screening a combinatorial phage display peptide library, serial subdomain deletion, and mutagenesis scanning. X-ray crystal structure of the A21 scFv fragment at 2.1 A resolution was also determined. A molecular model of Ag-Ab complex was then constructed based on the crystal structures of the A21 scFv and ErbB2 ECD. Some of biological functions of the A21 mAb and its derivative antibodies including their tumor cell growth inhibition and effects on the expression, internalization, and phosphorylation of ErbB2 receptor were also investigated. The results showed that A21 recognized a conformational epitope comprising a large region mostly from ErbB2 extracellular subdomain I with several surface-exposed residues important for the binding affinity. These data provide unique functional properties of A21 that are quite different from two broadly used anti-ErbB2 mAbs, Herceptin and 2C4. It suggested that the A21 epitope may be another valuable target for designing new anti-ErbB2 therapeutics.


  • Organizational Affiliation

    Lab of Cellular and Molecular Immunology, School of Life Sciences, University of Science and Technology of China, Hefei 230027, People's Republic of China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A21 single-chain antibody fragment against erbB2
A, B
264Mus musculusMutation(s): 0 
Gene Names: scA21
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.943α = 90
b = 86.63β = 90
c = 178.592γ = 90
Software Package:
Software NamePurpose
MAR345data collection
HKL-2000data reduction
MOLREPphasing
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2006-10-01 
  • Deposition Author(s): Zhu, Z.

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-01
    Type: Initial release
  • Version 1.1: 2008-01-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-08-09
    Changes: Advisory, Refinement description, Source and taxonomy
  • Version 1.4: 2017-08-16
    Changes: Refinement description
  • Version 1.5: 2017-10-18
    Changes: Refinement description
  • Version 1.6: 2023-10-25
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description