6BAH

Trastuzumab Fab v3 with 5-diphenyl meditope variant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

wwPDB Validation 3D Report Full Report



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: 10.1021/acs.bioconjchem.8b00284
  • Structures With Same Primary Citation

  • 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. ...

    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.


    Organizational Affiliation

    WuXi AppTec Company, Ltd. , Shanghai 200131, P. R. China.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Protein LE64Finegoldia magnaMutation(s): 5 
Find proteins for Q51918 (Finegoldia magna)
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Go to UniProtKB:  Q51918
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Immunoglobulin G binding protein AC54Staphylococcus aureusMutation(s): 0 
Gene Names: spa
Find proteins for P02976 (Staphylococcus aureus (strain NCTC 8325))
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Go to UniProtKB:  P02976
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Trastuzumab Fab light chain,Immunoglobulin kappa constantA214Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Find proteins for P01834 (Homo sapiens)
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Go to UniProtKB:  P01834
NIH Common Fund Data Resources
PHAROS  P01834
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Trastuzumab Fab heavy chain,IGH@ proteinB223Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 1 
Find proteins for Q6GMX6 (Homo sapiens)
Explore Q6GMX6 
Go to UniProtKB:  Q6GMX6
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
meditopeD13synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
2GX
Query on 2GX
DL-PEPTIDE LINKINGC15 H15 N O2PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.41α = 90
b = 105.15β = 90
c = 116.98γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-09-05
    Type: Initial release