8GKL

Crystal Structure of the Humanized MUC16 Specific Antibody huAR9.6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.269 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

Starting Models: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Basis for Multivalent MUC16 Recognition and Robust Anti-Pancreatic Cancer Activity of Humanized Antibody AR9.6.

Aguilar, E.N.Sagar, S.Murray, B.R.Rajesh, C.Lei, E.K.Michaud, S.A.Goodlett, D.R.Caffrey, T.C.Grandgenett, P.M.Swanson, B.Brooks, T.M.Black, A.R.van Faassen, H.Hussack, G.Henry, K.A.Hollingsworth, M.A.Brooks, C.L.Radhakrishnan, P.

(2024) Mol Cancer Ther 23: 836-853

  • DOI: https://doi.org/10.1158/1535-7163.MCT-23-0868
  • Primary Citation of Related Structures:  
    8GKJ, 8GKK, 8GKL

  • PubMed Abstract: 

    Mucin-16 (MUC16) is a target for antibody-mediated immunotherapy in pancreatic ductal adenocarcinoma (PDAC) among other malignancies. The MUC16-specific monoclonal antibody AR9.6 has shown promise for PDAC immunotherapy and imaging. Here, we report the structural and biological characterization of the humanized AR9.6 antibody (huAR9.6). The structure of huAR9.6 was determined in complex with a MUC16 SEA (Sea urchin sperm, Enterokinase, Agrin) domain. Binding of huAR9.6 to recombinant, shed, and cell-surface MUC16 was characterized, and anti-PDAC activity was evaluated in vitro and in vivo. HuAR9.6 bound a discontinuous, SEA domain epitope with an overall affinity of 88 nmol/L. Binding affinity depended on the specific SEA domain(s) present, and glycosylation modestly enhanced affinity driven by favorable entropy and enthalpy and via distinct transition state thermodynamic pathways. Treatment with huAR9.6 reduced the in vitro growth, migration, invasion, and clonogenicity of MUC16-positive PDAC cells and patient-derived organoids (PDO). HuAR9.6 blocked MUC16-mediated ErbB and AKT activation in PDAC cells, PDOs, and patient-derived xenografts and induced antibody-dependent cellular cytotoxicity and complement-dependent cytotoxicity. More importantly, huAR9.6 treatment caused substantial PDAC regression in subcutaneous and orthotopic tumor models. The mechanism of action of huAR9.6 may depend on dense avid binding to homologous SEA domains on MUC16. The results of this study validate the translational therapeutic potential of huAR9.6 against MUC16-positive PDACs.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, California State University Fresno, Fresno, California.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mucin-16A [auth E]127Homo sapiensMutation(s): 0 
Gene Names: MUC16CA125
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WXI7 (Homo sapiens)
Explore Q8WXI7 
Go to UniProtKB:  Q8WXI7
PHAROS:  Q8WXI7
GTEx:  ENSG00000181143 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WXI7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MUC16 antibody AR9.6 Fab light chainB [auth L]218Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
MUC16 antibody AR9.6 Fab heavy chainC [auth H]233Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.269 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.47α = 90
b = 124.36β = 90
c = 235.43γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR15CA242349

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-20
    Type: Initial release
  • Version 1.1: 2024-10-02
    Changes: Database references
  • Version 1.2: 2024-10-23
    Changes: Structure summary