9Z3B | pdb_00009z3b

Structure C-terminal human Mesothelin Peptide bound to MSLNB703 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 
    0.278 (Depositor), 0.268 (DCC) 
  • R-Value Work: 
    0.227 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 
    0.229 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

JNJ-79032421, a Novel Membrane-restricted Mesothelin-targeting T-cell-engaging Bispecific Antibody for the Treatment of Mesothelin-positive Cancers.

Smans, K.Nesspor, T.De Breucker, S.van Heerde, E.Valckx, A.Van Slycken, N.Sproesser, K.Mattson Cypert, B.Packman, K.Chu, G.Fisher, J.Mazzanti, N.Petley, T.Chan, W.Del Rosario, B.Liu, T.Ember, S.Shaffer, P.L.Clawson, J.S.Bauml, J.M.Moores, S.Laquerre, S.Gavine, P.R.

(2026) Mol Cancer Ther 

  • DOI: https://doi.org/10.1158/1535-7163.MCT-25-0665
  • Primary Citation Related Structures: 
    9Z3B

  • PubMed Abstract: 

    Mesothelin (MSLN) is a cell-membrane-anchored glycoprotein overexpressed in several cancers including pancreatic cancer, ovarian cancer, and mesothelioma. MSLN is protease-cleaved at the membrane-proximal region, releasing shed MSLN (sMSLN) into the tumor microenvironment, leaving behind a membrane-bound stub. sMSLN in the tumor microenvironment is hypothesized to create a 'sink' that could limit tumor binding of MSLN-targeted anticancer therapies. We describe JNJ-79032421, a bispecific antibody targeting cluster of differentiation (CD)3 on T cells and the membrane-restricted, non-shed region of full-length MSLN on cancer cells. Crystal structure analysis confirmed JNJ-79032421 binding to the membrane-restricted, non-shed C-terminal region of MSLN. Using Western blot, enzyme-linked immunosorbent assay, fluorescence-activated cell sorting, and immunohistochemistry, elevated levels of sMSLN were detected in blood, serosal fluids, and tumor tissue of patients and tended to increase with MSLN tumor expression. Binding and cytotoxicity of JNJ-79032421 against cancer cell lines was unaffected by the presence of sMSLN. In cancer cell lines and cell-line-derived and patient-derived xenograft mouse models, increasing levels of MSLN expression led to increased JNJ-79032421 potency. In contrast, MSLNxCD3 bispecific antibodies whose binding is non membrane restricted demonstrated a loss of cytotoxicity in the presence of sMSLN. This 'sink' effect was most pronounced for high-affinity non-membrane-restricted bispecific antibodies. Increases of CD45+ and CD8+ T-cell infiltrates, as well as CD8+ T-cell activation, observed in xenograft tumor tissues were time and JNJ-79032421 dose dependent. Overall, these data suggest that JNJ-79032421 may offer meaningful clinical activity by avoiding binding to sMSLN.


  • Organizational Affiliation
    • Johnson & Johnson (United States) Beerse Belgium.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MSLNB703 Light Chain
A, C, E, G
220Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MSLNB703 Heavy Chain
B, D, F, H
231Homo sapiensMutation(s): 0 
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Mesothelin
I, J, K, L
17Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q13421 (Homo sapiens)
Explore Q13421 
Go to UniProtKB:  Q13421
PHAROS:  Q13421
GTEx:  ENSG00000102854 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13421
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free:  0.278 (Depositor), 0.268 (DCC) 
  • R-Value Work:  0.227 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.151α = 77.18
b = 79.744β = 89.73
c = 86.774γ = 89.84
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-21
    Type: Initial release
  • Version 1.1: 2026-03-25
    Changes: Database references