9O6N | pdb_00009o6n

Structure of Siglec-10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 
    0.259 (Depositor), 0.259 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Structural basis for sialoglycan recognition by the immune inhibitory receptor Siglec-10.

Medina, E.Mason, C.Tran, T.H.Julia, E.P.Ming, Q.Taibi, L.M.Hwu, P.Maute, R.L.Burg, J.S.Luca, V.C.

(2026) Structure 34: 768-777.e5

  • DOI: https://doi.org/10.1016/j.str.2026.01.018
  • Primary Citation Related Structures: 
    9O6J, 9O6N, 9O6O

  • PubMed Abstract: 

    Sialic acid-binding immunoglobulin-like lectin 10 (Siglec-10) inhibits immune cell function by sensing the presence of sialylated glycoproteins. Here, we determined structures of Siglec-10 bound to sialyllactose (SL) ligands to visualize the molecular recognition events underlying Siglec-10 signaling. The structures reveal that domain 1 (D1) of Siglec-10 engages SL using a non-conserved, selectivity determining CC' loop. Siglec-10 binds α2,3- and α2,6-linked SL with similar affinities despite minor additional contacts between D1 and the α2,3-SL galactose. Homodimerization of Siglec-10 is mediated by a hydrophobic domain 2 (D2) interface, and mutation of this interface ablates cellular binding similarly to mutations in the CC' loop and glycan-binding site. Surprisingly, knockout of the putative Siglec-10 ligand, CD24, did not affect binding to breast cancer cells, indicating that Siglec-10 has a broader-than-expected glycoprotein recognition profile. These findings emphasize how a complex interplay between Siglec-10 multimerization and ligand engagement facilitate cell surface interactions.


  • Organizational Affiliation
    • Department of Immunology, Moffitt Cancer Center, Tampa, FL 33612, USA; Cancer Biology PhD Program, University of South Florida, Tampa, FL 33612, USA.

Macromolecule Content 

  • Total Structure Weight: 75.72 kDa 
  • Atom Count: 5,296 
  • Modeled Residue Count: 654 
  • Deposited Residue Count: 657 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Sialic acid-binding Ig-like lectin 10
A, B, C
219Homo sapiensMutation(s): 0 
Gene Names: SIGLEC10SLG2UNQ477/PRO940
UniProt & NIH Common Fund Data Resources
Find proteins for Q96LC7 (Homo sapiens)
Explore Q96LC7 
Go to UniProtKB:  Q96LC7
PHAROS:  Q96LC7
GTEx:  ENSG00000142512 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96LC7
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q96LC7-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
(Subject of Investigation/LOI)

Query on NAG



Download:Ideal Coordinates CCD File
G [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
FLC
(Subject of Investigation/LOI)

Query on FLC



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
J [auth C]
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
GOL

Query on GOL



Download:Ideal Coordinates CCD File
H [auth B],
K [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
I [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free:  0.259 (Depositor), 0.259 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.83α = 90
b = 83.83β = 90
c = 484.4γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM133482

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-25
    Type: Initial release
  • Version 1.1: 2026-09-09
    Changes: Database references