4HKZ

Trastuzumab Fab complexed with Protein L and Protein A fragments


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Identification and grafting of a unique peptide-binding site in the Fab framework of monoclonal antibodies.

Donaldson, J.M.Zer, C.Avery, K.N.Bzymek, K.P.Horne, D.A.Williams, J.C.

(2013) Proc.Natl.Acad.Sci.USA 110: 17456-17461

  • DOI: 10.1073/pnas.1307309110
  • Primary Citation of Related Structures:  4GW1, 4GW5, 4HJG, 4IOI

  • PubMed Abstract: 
  • Capitalizing on their extraordinary specificity, monoclonal antibodies (mAbs) have become one of the most reengineered classes of biological molecules. A major goal in many of these engineering efforts is to add new functionality to the parental mAb, ...

    Capitalizing on their extraordinary specificity, monoclonal antibodies (mAbs) have become one of the most reengineered classes of biological molecules. A major goal in many of these engineering efforts is to add new functionality to the parental mAb, including the addition of cytotoxins and imaging agents for medical applications. Herein, we present a unique peptide-binding site within the central cavity of the fragment antigen binding framework region of the chimeric, anti-epidermal growth factor receptor mAb cetuximab. We demonstrate through diffraction methods, biophysical studies, and sequence analysis that this peptide, a meditope, has moderate affinity for the Fab, is specific to cetuximab (i.e., does not bind to human IgGs), and has no significant effect on antigen binding. We further demonstrate by diffraction studies and biophysical methods that the meditope binding site can be grafted onto the anti-human epidermal growth factor receptor 2 mAb trastuzumab, and that the antigen binding affinity of the grafted trastuzumab is indistinguishable from the parental mAb. Finally, we demonstrate a bivalent meditope variant binds specifically and stably to antigen-bearing cells only in the presence of the meditope-enabled mAbs. Collectively, this finding and the subsequent characterization and engineering efforts indicate that this unique interface could serve as a noncovalent "linker" for any meditope-enabled mAb with applications in multiple mAb-based technologies including diagnostics, imaging, and therapeutic delivery.


    Organizational Affiliation

    Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Trastuzumab light chain
A
213N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Trastuzumab heavy chain
B
221N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Immunoglobulin G-binding protein A
H
54Staphylococcus aureus (strain Mu50 / ATCC 700699)Gene Names: spa
Find proteins for P0A015 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Go to UniProtKB:  P0A015
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Protein L fragment
E
63Finegoldia magnaN/A
Find proteins for Q51918 (Finegoldia magna)
Go to UniProtKB:  Q51918
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.162 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.520α = 90.00
b = 104.670β = 90.00
c = 117.550γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
Blu-Icedata collection
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-09
    Type: Initial release
  • Version 1.1: 2013-10-23
    Type: Database references
  • Version 1.2: 2013-11-06
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description