6BBD

Structure of N-glycosylated porcine surfactant protein-D complexed with glycerol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Lectin-mediated binding and sialoglycans of porcine surfactant protein D synergistically neutralize influenza A virus.

van Eijk, M.Rynkiewicz, M.J.Khatri, K.Leymarie, N.Zaia, J.White, M.R.Hartshorn, K.L.Cafarella, T.R.van Die, I.Hessing, M.Seaton, B.A.Haagsman, H.P.

(2018) J Biol Chem 293: 10646-10662

  • DOI: https://doi.org/10.1074/jbc.RA117.001430
  • Primary Citation of Related Structures:  
    6BBD, 6BBE

  • PubMed Abstract: 

    Innate immunity is critical in the early containment of influenza A virus (IAV) infection, and surfactant protein D (SP-D) plays a crucial role in the pulmonary defense against IAV. In pigs, which are important intermediate hosts during the generation of pandemic IAVs, SP-D uses its unique carbohydrate recognition domain (CRD) to interact with IAV. An N -linked CRD glycosylation provides interactions with the sialic acid-binding site of IAV, and a tripeptide loop at the lectin-binding site facilitates enhanced interactions with IAV glycans. Here, to investigate both mechanisms of IAV neutralization in greater detail, we produced an N -glycosylated neck-CRD fragment of porcine SP-D (RpNCRD) in HEK293 cells. X-ray crystallography disclosed that the N -glycan did not alter the CRD backbone structure, including the lectin site conformation, but revealed a potential second nonlectin-binding site for glycans. IAV hemagglutination inhibition, IAV aggregation, and neutralization of IAV infection studies showed that RpNCRD, unlike the human analogue RhNCRD, exhibits potent neutralizing activity against pandemic A/Aichi/68 (H3N2), enabled by both porcine-specific structural features of its CRD. MS analysis revealed an N -glycan site-occupancy of >98% at Asn-303 of RpNCRD with complex-type, heterogeneously branched and predominantly α(2,3)-sialylated oligosaccharides. Glycan-binding array data characterized both RpNCRD and RhNCRD as mannose-type lectins. RpNCRD also bound Lewis Y structures, whereas RhNCRD bound polylactosamine-containing glycans. The presence of the N -glycan in the CRD increases the glycan-binding specificity of RpNCRD. These insights increase our understanding of porcine-specific innate defense against pandemic IAV and may inform the design of recombinant SP-D-based antiviral drugs.


  • Organizational Affiliation

    the Departments of Physiology and Biophysics and.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pulmonary surfactant-associated protein D154Sus scrofaMutation(s): 0 
Gene Names: SFTPD
UniProt
Find proteins for Q9N1X4 (Sus scrofa)
Explore Q9N1X4 
Go to UniProtKB:  Q9N1X4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9N1X4
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G12045WP
GlyCosmos:  G12045WP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.205 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.798α = 90
b = 66.798β = 90
c = 64.974γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata collection
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Open Technology Program GrantNetherlands10388

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-23
    Type: Initial release
  • Version 1.1: 2018-05-30
    Changes: Data collection, Database references
  • Version 1.2: 2018-07-18
    Changes: Data collection, Database references, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary