7ZOR

Crystal structure of anti-Siglec-15 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.93 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.232 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 7ZOZ


Literature

Structural insights into Siglec-15 reveal glycosylation dependency for its interaction with T cells through integrin CD11b.

Lenza, M.P.Egia-Mendikute, L.Antonana-Vildosola, A.Soares, C.O.Coelho, H.Corzana, F.Bosch, A.Manisha, P.Quintana, J.I.Oyenarte, I.Unione, L.Moure, M.J.Azkargorta, M.Atxabal, U.Sobczak, K.Elortza, F.Sutherland, J.D.Barrio, R.Marcelo, F.Jimenez-Barbero, J.Palazon, A.Ereno-Orbea, J.

(2023) Nat Commun 14: 3496-3496

  • DOI: https://doi.org/10.1038/s41467-023-39119-8
  • Primary Citation of Related Structures:  
    7ZOR, 7ZOZ

  • PubMed Abstract: 

    Sialic acid-binding Ig-like lectin 15 (Siglec-15) is an immune modulator and emerging cancer immunotherapy target. However, limited understanding of its structure and mechanism of action restrains the development of drug candidates that unleash its full therapeutic potential. In this study, we elucidate the crystal structure of Siglec-15 and its binding epitope via co-crystallization with an anti-Siglec-15 blocking antibody. Using saturation transfer-difference nuclear magnetic resonance (STD-NMR) spectroscopy and molecular dynamics simulations, we reveal Siglec-15 binding mode to α(2,3)- and α(2,6)-linked sialic acids and the cancer-associated sialyl-Tn (STn) glycoform. We demonstrate that binding of Siglec-15 to T cells, which lack STn expression, depends on the presence of α(2,3)- and α(2,6)-linked sialoglycans. Furthermore, we identify the leukocyte integrin CD11b as a Siglec-15 binding partner on human T cells. Collectively, our findings provide an integrated understanding of the structural features of Siglec-15 and emphasize glycosylation as a crucial factor in controlling T cell responses.


  • Organizational Affiliation

    Chemical Glycobiology lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Anti-siglec15 FAB HCA [auth I],
C [auth H]
225Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Anti-siglec15 FAB LCB [auth M],
D [auth L]
214Homo sapiensMutation(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: 3.93 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.232 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.02α = 90
b = 60.681β = 107.86
c = 131.258γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
H2020 Marie Curie Actions of the European CommissionEuropean Union--
Spanish Ministry of Science, Innovation, and UniversitiesSpain--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-28
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection, Refinement description