6B9Z

Trastuzumab Fab v3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Template-Catalyzed, Disulfide Conjugation of Monoclonal Antibodies Using a Natural Amino Acid Tag.

King, J.D.Ma, Y.Kuo, Y.C.Bzymek, K.P.Goodstein, L.H.Meyer, K.Moore, R.E.Crow, D.Colcher, D.M.Singh, G.Horne, D.A.Williams, J.C.

(2018) Bioconjug Chem 29: 2074-2081

  • DOI: https://doi.org/10.1021/acs.bioconjchem.8b00284
  • Primary Citation of Related Structures:  
    6B9Y, 6B9Z, 6BAE, 6BAH

  • PubMed Abstract: 

    The high specificity and favorable pharmacological properties of monoclonal antibodies (mAbs) have prompted significant interest in re-engineering this class of molecules to add novel functionalities for enhanced therapeutic and diagnostic potential. Here, we used the high affinity, meditope-Fab interaction to template and drive the rapid, efficient, and stable site-specific formation of a disulfide bond. We demonstrate that this template-catalyzed strategy provides a consistent and reproducible means to conjugate fluorescent dyes, cytotoxins, or "click" chemistry handles to meditope-enabled mAbs (memAbs) and memFabs. More importantly, we demonstrate this covalent functionalization is achievable using natural amino acids only, opening up the opportunity to genetically encode cysteine meditope "tags" to biologics. As proof of principle, genetically encoded, cysteine meditope tags were added to the N- and/or C-termini of fluorescent proteins, nanobodies, and affibodies, each expressed in bacteria, purified to homogeneity, and efficiently conjugated to different memAbs and meFabs. We further show that multiple T-cell and Her2-targeting bispecific molecules using this strategy potently activate T-cell signaling pathways in vitro. Finally, the resulting products are highly stable as evidenced by serum stability assays (>14 d at 37 °C) and in vivo imaging of tumor xenographs. Collectively, the platform offers the opportunity to build and exchange an array of functional moieties, including protein biologics, among any cysteine memAb or Fab to rapidly create, test, and optimize stable, multifunctional biologics.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Trastuzumab Fab light chain214Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01834 (Homo sapiens)
Explore P01834 
Go to UniProtKB:  P01834
PHAROS:  P01834
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UniProt GroupP01834
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Trastuzumab Fab heavy chain223Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 2 
UniProt
Find proteins for S6B291 (Homo sapiens)
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Go to UniProtKB:  S6B291
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UniProt GroupS6B291
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein LC [auth E]64Finegoldia magnaMutation(s): 5 
UniProt
Find proteins for Q51918 (Finegoldia magna)
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UniProt GroupQ51918
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Immunoglobulin G binding protein AD [auth C]54Staphylococcus aureusMutation(s): 0 
Gene Names: spa
UniProt
Find proteins for P02976 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Go to UniProtKB:  P02976
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UniProt GroupP02976
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
B
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.49α = 90
b = 105.29β = 90
c = 117.15γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-05
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2023-11-15
    Changes: Data collection