3G83

Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with alpha 1,2 dimannose.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Recognition of mannosylated ligands and influenza A virus by human surfactant protein D: contributions of an extended site and residue 343.

Crouch, E.Hartshorn, K.Horlacher, T.McDonald, B.Smith, K.Cafarella, T.Seaton, B.Seeberger, P.H.Head, J.

(2009) Biochemistry 48: 3335-3345

  • DOI: 10.1021/bi8022703
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Surfactant protein D (SP-D) plays important roles in antiviral host defense. Although SP-D shows a preference for glucose/maltose, the protein also recognizes d-mannose and a variety of mannose-rich microbial ligands. This latter preference prompted ...

    Surfactant protein D (SP-D) plays important roles in antiviral host defense. Although SP-D shows a preference for glucose/maltose, the protein also recognizes d-mannose and a variety of mannose-rich microbial ligands. This latter preference prompted an examination of the mechanisms of mannose recognition, particularly as they relate to high-mannose viral glycans. Trimeric neck plus carbohydrate recognition domains from human SP-D (hNCRD) preferred alpha1-2-linked dimannose (DM) over the branched trimannose (TM) core, alpha1-3 or alpha1-6 DM, or D-mannose. Previous studies have shown residues flanking the carbohydrate binding site can fine-tune ligand recognition. A mutant with valine at 343 (R343V) showed enhanced binding to mannan relative to wild type and R343A. No alteration in affinity was observed for D-mannose or for alpha1-3- or alpha1-6-linked DM; however, substantially increased affinity was observed for alpha1-2 DM. Both proteins showed efficient recognition of linear and branched subdomains of high-mannose glycans on carbohydrate microarrays, and R343V showed increased binding to a subset of the oligosaccharides. Crystallographic analysis of an R343V complex with 1,2-DM showed a novel mode of binding. The disaccharide is bound to calcium by the reducing sugar ring, and a stabilizing H-bond is formed between the 2-OH of the nonreducing sugar ring and Arg349. Although hNCRDs show negligible binding to influenza A virus (IAV), R343V showed markedly enhanced viral neutralizing activity. Hydrophobic substitutions for Arg343 selectively blocked binding of a monoclonal antibody (Hyb 246-05) that inhibits IAV binding activity. Our findings demonstrate an extended ligand binding site for mannosylated ligands and the significant contribution of the 343 side chain to specific recognition of multivalent microbial ligands, including high-mannose viral glycans.


    Organizational Affiliation

    Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, USA. crouch@path.wustl.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pulmonary surfactant-associated protein D
A, B, C
160Homo sapiensMutation(s): 0 
Gene Names: SFTPD (COLEC7, PSPD, SFTP4)
Find proteins for P35247 (Homo sapiens)
Go to Gene View: SFTPD
Go to UniProtKB:  P35247
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, B, C
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 55.754α = 90.00
b = 108.774β = 91.58
c = 56.011γ = 90.00
Software Package:
Software NamePurpose
CBASSdata collection
SCALEPACKdata scaling
DENZOdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-02-11 
  • Released Date: 2009-03-17 
  • Deposition Author(s): Head, J.F.

Revision History 

  • Version 1.0: 2009-03-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description