9MNB | pdb_00009mnb

Beta1-tryptase monomer bound to inhibitory Fabs E82.AS and E104.v2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: in silico, experimental
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Literature

Complete inhibition of beta-tryptase by tetramer dissociation and active site allostery due to a single antibody residue.

Maun, H.R.Azumaya, C.M.Walters, B.T.Vij, R.Morando, A.Loyet, K.M.Koerber, J.T.Rohou, A.Lazarus, R.A.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-70491-3
  • Primary Citation Related Structures: 
    9MNB

  • PubMed Abstract: 

    Human β-tryptase, a tetrameric trypsin-like serine protease, is an important mediator of inflammatory responses in asthma, allergy and other diseases. Here we report an anti-β-tryptase antibody with a superior mechanism of action compared to others since it not only inhibits tetrameric β-tryptase, but also completely inhibits monomeric β-tryptase activity. The antibody binds to an exosite that causes tetramer dissociation as either an IgG or Fab and, in addition, allosterically alters the substrate binding cleft on monomers, thus preventing substrate binding and proteolysis. We solve the cryoEM structure of the complex, generate biochemical data and engineer point mutations to elucidate the allosteric path of inhibition. This ultimately reveals a single Asp to Gly mutation in CDR-L3 that only slightly impacts binding affinity, but completely eliminates inhibitory activity. Finally, we improve antibody inhibitory potency up to 4.7-fold by structure-based design creating new charge-charge interactions. This antibody may have enhanced efficacy and potential to assess the relevance of β-tryptase, including monomers, in biological and clinical settings.


  • Organizational Affiliation
    • Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, CA, USA. maun.henry@gene.com.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Light chain of E104.v2 FabA [auth L]216Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tryptase alpha/beta-1B [auth A]245Homo 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 
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UniProt GroupQ15661
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy chain of E104v2 FabC [auth H]221Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Light chain of E82.AS FabD [auth F]220Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy chain of E82.AS Fab216Homo sapiensMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Anti-human kappa light chain VHHF [auth K]120Lama glamaMutation(s): 0 
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
UNK
Query on UNK
F [auth K]L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2026-04-22
    Type: Initial release