9FY8 | pdb_00009fy8

L2A5 Fab in complex with STn-Thr


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 
    0.306 (Depositor), 0.304 (DCC) 
  • R-Value Work: 
    0.248 (Depositor), 0.248 (DCC) 
  • R-Value Observed: 
    0.251 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

Decoding the Molecular Basis of the Specificity of an Anti-sTn Antibody.

Soares, C.O.Laugieri, M.E.Grosso, A.S.Natale, M.Coelho, H.Behren, S.Yu, J.Cai, H.Franconetti, A.Oyenarte, I.Magnasco, M.Gimeno, A.Ramos, N.Chai, W.Corzana, F.Westerlind, U.Jimenez-Barbero, J.Palma, A.S.Videira, P.A.Ereno-Orbea, J.Marcelo, F.

(2025) JACS Au 5: 225-236

  • DOI: https://doi.org/10.1021/jacsau.4c00921
  • Primary Citation of Related Structures:  
    9FXT, 9FY8

  • PubMed Abstract: 

    The mucin O -glycan sialyl Tn antigen (sTn, Neu5Acα2-6GalNAcα1- O -Ser/Thr) is an antigen associated with different types of cancers, often linked with a higher risk of metastasis and poor prognosis. Despite efforts to develop anti-sTn antibodies with high specificity for diagnostics and immunotherapy, challenges in eliciting high-affinity antibodies for glycan structures have limited their effectiveness, leading to low titers and short protection durations. Experimental structural insights into anti-sTn antibody specificity are lacking, hindering their optimization for cancer cell recognition. In this study, we used a comprehensive structural approach, combining X-ray crystallography, NMR spectroscopy, computational methods, glycan/glycopeptide microarrays, and biophysical techniques, to thoroughly investigate the molecular basis of sTn recognition by L2A5, a novel preclinical anti-sTn monoclonal antibody (mAb). Our data unequivocally show that the L2A5 fragment antigen-binding (Fab) specifically binds to core sTn moieties. NMR and X-ray structural data suggest a similar binding mode for the complexes formed by the sTn moiety linked to Ser or Thr and the L2A5 Fab. The sugar moieties are similarly oriented in the paratope of mAb, with the Neu5Ac moiety establishing key interactions with the receptor and the GalNAc moiety providing additional contacts. Furthermore, L2A5 exhibits fine specificity toward cancer-related MUC1 and MUC4 mucin-derived sTn glycopeptides, which might contribute to its selective targeting against tumor cells. This newfound knowledge holds promise for the rational improvement and potential application of this anti-sTn antibody in diagnosis and targeted therapy against sTn expressing cancers such as breast, colorectal, and bladder cancer, improving patient care.


  • Organizational Affiliation
    • UCIBIO-Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, NOVA University Lisbon, 2829-516 Caparica, Portugal.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L2A5 Fab Heavy chainA [auth B],
D [auth I]
216Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
L2A5 Fab Light ChainB [auth C],
E [auth L]
215Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Human anti kappa variable heavy chainC [auth D],
F [auth V]
126Homo sapiensMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-2-acetamido-2-deoxy-alpha-D-galactopyranoseG [auth A],
H [auth E]
2N/A
Glycosylation Resources
GlyTouCan:  G36123IU
GlyCosmos:  G36123IU
GlyGen:  G36123IU
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free:  0.306 (Depositor), 0.304 (DCC) 
  • R-Value Work:  0.248 (Depositor), 0.248 (DCC) 
  • R-Value Observed: 0.251 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.331α = 90
b = 128.144β = 98.17
c = 98.896γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agencia Estatal de Investigacion (AEI)Spain--
European CommissionEuropean Union101079417

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-12
    Type: Initial release