4DN8

Structure of porcine surfactant protein D neck and carbohydrate recognition domain complexed with mannose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

A Unique Sugar-binding Site Mediates the Distinct Anti-influenza Activity of Pig Surfactant Protein D.

van Eijk, M.Rynkiewicz, M.J.White, M.R.Hartshorn, K.L.Zou, X.Schulten, K.Luo, D.Crouch, E.C.Cafarella, T.R.Head, J.F.Haagsman, H.P.Seaton, B.A.

(2012) J Biol Chem 287: 26666-26677

  • DOI: https://doi.org/10.1074/jbc.M112.368571
  • Primary Citation of Related Structures:  
    4DN8

  • PubMed Abstract: 

    Pigs can act as intermediate hosts by which reassorted influenza A virus (IAV) strains can be transmitted to humans and cause pandemic influenza outbreaks. The innate host defense component surfactant protein D (SP-D) interacts with glycans on the hemagglutinin of IAV and contributes to protection against IAV infection in mammals. This study shows that a recombinant trimeric neck lectin fragment derived from porcine SP-D (pSP-D) exhibits profound inhibitory activity against IAV, in contrast to comparable fragments derived from human SP-D. Crystallographic analysis of the pSP-D fragment complexed with a viral sugar component shows that a unique tripeptide loop alters the lectin site conformation of pSP-D. Molecular dynamics simulations highlight the role of this flexible loop, which adopts a more stable conformation upon sugar binding and may facilitate binding to viral glycans through contact with distal portions of the branched mannoside. The combined data demonstrate that porcine-specific structural features of SP-D contribute significantly to its distinct anti-IAV activity. These findings could help explain why pigs serve as important reservoirs for newly emerging pathogenic IAV strains.


  • Organizational Affiliation

    Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pulmonary surfactant-associated protein D156Sus scrofaMutation(s): 1 
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.203 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.024α = 90
b = 66.024β = 90
c = 66.018γ = 120
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASERphasing
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-20
    Type: Initial release
  • Version 1.1: 2012-08-22
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2021-05-19
    Changes: Source and taxonomy, Structure summary
  • Version 1.4: 2023-09-13
    Changes: Advisory, Data collection, Database references, Refinement description