6VVU

Anti-Tryptase fab E104.v1 bound to tryptase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Bivalent antibody pliers inhibit beta-tryptase by an allosteric mechanism dependent on the IgG hinge.

Maun, H.R.Vij, R.Walters, B.T.Morando, A.Jackman, J.K.Wu, P.Estevez, A.Chen, X.Franke, Y.Lipari, M.T.Dennis, M.S.Kirchhofer, D.Ciferri, C.Loyet, K.M.Yi, T.Eigenbrot, C.Lazarus, R.A.Koerber, J.T.

(2020) Nat Commun 11: 6435-6435

  • DOI: https://doi.org/10.1038/s41467-020-20143-x
  • Primary Citation of Related Structures:  
    6VVU

  • PubMed Abstract: 

    Human β-tryptase, a tetrameric trypsin-like serine protease, is an important mediator of allergic inflammatory responses in asthma. Antibodies generally inhibit proteases by blocking substrate access by binding to active sites or exosites or by allosteric modulation. The bivalency of IgG antibodies can increase potency via avidity, but has never been described as essential for activity. Here we report an inhibitory anti-tryptase IgG antibody with a bivalency-driven mechanism of action. Using biochemical and structural data, we determine that four Fabs simultaneously occupy four exosites on the β-tryptase tetramer, inducing allosteric changes at the small interface. In the presence of heparin, the monovalent Fab shows essentially no inhibition, whereas the bivalent IgG fully inhibits β-tryptase activity in a hinge-dependent manner. Our results suggest a model where the bivalent IgG acts akin to molecular pliers, pulling the tetramer apart into inactive β-tryptase monomers, and may provide an alternative strategy for antibody engineering.


  • Organizational Affiliation

    Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tryptase alpha/beta-1A,
B,
C [auth D],
D [auth C]
275Homo sapiensMutation(s): 0 
Gene Names: TPSAB1TPS1TPS2TPSB1
EC: 3.4.21.59
UniProt & NIH Common Fund Data Resources
Find proteins for Q15661 (Homo sapiens)
Explore Q15661 
Go to UniProtKB:  Q15661
PHAROS:  Q15661
GTEx:  ENSG00000172236 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15661
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab E104.v1 heavy chain
E, G, H, J
230Homo sapiensMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab E104.v1 light chain
F, I, K, L
217Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.573α = 90
b = 168.811β = 109.97
c = 114.652γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-30
    Type: Initial release
  • Version 1.1: 2021-01-13
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description