2N7A | pdb_00002n7a

Solution structure of the human Siglec-8 lectin domain


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 500 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

Validation slider image for 2N7A

This is version 1.5 of the entry. See complete history

Literature

Structural basis for sulfation-dependent self-glycan recognition by the human immune-inhibitory receptor Siglec-8.

Propster, J.M.Yang, F.Rabbani, S.Ernst, B.Allain, F.H.Schubert, M.

(2016) Proc Natl Acad Sci U S A 113: E4170-E4179

  • DOI: https://doi.org/10.1073/pnas.1602214113
  • Primary Citation Related Structures: 
    2N7A, 2N7B

  • PubMed Abstract: 

    Siglec-8 is a human immune-inhibitory receptor that, when engaged by specific self-glycans, triggers eosinophil apoptosis and inhibits mast cell degranulation, providing an endogenous mechanism to down-regulate immune responses of these central inflammatory effector cells. Here we used solution NMR spectroscopy to dissect the fine specificity of Siglec-8 toward different sialylated and sulfated carbohydrate ligands and determined the structure of the Siglec-8 lectin domain in complex with its prime glycan target 6'-sulfo sialyl Lewis(x) A canonical motif for sialic acid recognition, extended by a secondary motif formed by unique loop regions, recognizing 6-O-sulfated galactose dictates tight specificity distinct from other Siglec family members and any other endogenous glycan recognition receptors. Structure-guided mutagenesis revealed key contacts of both interfaces to be equally essential for binding. Our work provides critical structural and mechanistic insights into how Siglec-8 selectively recognizes its glycan target, rationalizes the functional impact of site-specific glycan sulfation in modulating this lectin-glycan interaction, and will enable the rational design of Siglec-8-targeted agonists to treat eosinophil- and mast cell-related allergic and inflammatory diseases, such as asthma.


  • Organizational Affiliation
    • Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland;

Macromolecule Content 

  • Total Structure Weight: 16.67 kDa 
  • Atom Count: 1,175 
  • Modeled Residue Count: 145 
  • Deposited Residue Count: 145 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Sialic acid-binding Ig-like lectin 8145Homo sapiensMutation(s): 1 
Gene Names: SAF2SIGLEC8
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NYZ4 (Homo sapiens)
Explore Q9NYZ4 
Go to UniProtKB:  Q9NYZ4
PHAROS:  Q9NYZ4
GTEx:  ENSG00000105366 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NYZ4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 500 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-06
    Type: Initial release
  • Version 1.1: 2016-07-27
    Changes: Database references
  • Version 1.2: 2016-08-03
    Changes: Database references
  • Version 1.3: 2016-10-12
    Changes: Structure summary
  • Version 1.4: 2023-06-14
    Changes: Data collection, Database references, Other
  • Version 1.5: 2024-11-20
    Changes: Data collection, Database references, Structure summary