4E52

Crystal structure of Haemophilus Eagan 4A polysaccharide bound human lung surfactant protein D


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of a Complex of Surfactant Protein D (SP-D) and Haemophilus influenzae Lipopolysaccharide Reveals Shielding of Core Structures in SP-D-Resistant Strains.

Clark, H.W.Mackay, R.M.Deadman, M.E.Hood, D.W.Madsen, J.Moxon, E.R.Townsend, J.P.Reid, K.B.Ahmed, A.Shaw, A.J.Greenhough, T.J.Shrive, A.K.

(2016) Infect.Immun. 84: 1585-1592

  • DOI: 10.1128/IAI.01239-15

  • PubMed Abstract: 
  • The carbohydrate recognition domains (CRDs) of lung collectin surfactant protein D (SP-D) recognize sugar patterns on the surface of lung pathogens and promote phagocytosis. Using Haemophilus influenzae Eagan strains expressing well-characterized lip ...

    The carbohydrate recognition domains (CRDs) of lung collectin surfactant protein D (SP-D) recognize sugar patterns on the surface of lung pathogens and promote phagocytosis. Using Haemophilus influenzae Eagan strains expressing well-characterized lipopolysaccharide (LPS) surface structures of various levels of complexity, we show that bacterial recognition and binding by SP-D is inversely related to LPS chain extent and complexity. The crystal structure of a biologically active recombinant trimeric SP-D CRD complexed with a delipidated Eagan 4A LPS suggests that efficient LPS recognition by SP-D requires multiple binding interactions utilizing the three major ligand-binding determinants in the SP-D binding pocket, with Ca-dependent binding of inner-core heptose accompanied by interaction of anhydro-Kdo (4,7-anhydro-3-deoxy-d-manno-oct-2-ulosonic acid) with Arg343 and Asp325. Combined with enzyme-linked immunosorbent assays (ELISAs) and fluorescence-activated cell sorter (FACS) binding analyses, our results show that extended LPS structures previously thought to be targets for collectins are important in shielding the more vulnerable sites in the LPS core, revealing a mechanism by which pathogens with complex LPS extensions efficiently evade a first-line mucosal innate immune defense. The structure also reveals for the first time the dominant form of anhydro-Kdo.


    Related Citations: 
    • High-resolution structural insights into ligand binding and immune cell recognition by human lung surfactant protein D.
      Shrive, A.K.,Tharia, H.A.,Strong, P.,Kishore, U.,Burns, I.,Rizkallah, P.J.,Reid, K.B.,Greenhough, T.J.
      (2003) J.Mol.Biol. 331: 509
    • Structural characterisation of ligand-binding determinants in human lung surfactant protein D: influence of Asp325.
      Shrive, A.K.,Martin, C.,Burns, I.,Paterson, J.M.,Martin, J.D.,Townsend, J.P.,Waters, P.,Clark, H.W.,Kishore, U.,Reid, K.B.,Greenhough, T.J.
      (2009) J.Mol.Biol. 394: 776


    Organizational Affiliation

    University of Southampton, Department of Child Health, Division of Clinical and Experimental Sciences, Faculty of Medicine, Sir Henry Wellcome Laboratories, Southampton General Hospital, Southampton, United Kingdom Institute for Life Sciences, University of Southampton, Southampton, United Kingdom National Institute for Health Research, Southampton Respiratory Biomedical Research Unit, Southampton Centre for Biomedical Research, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pulmonary surfactant-associated protein D
A, B, C
177Homo sapiensGene Names: SFTPD (COLEC7, PSPD, SFTP4)
Find proteins for P35247 (Homo sapiens)
Go to Gene View: SFTPD
Go to UniProtKB:  P35247
Small Molecules
Ligands 3 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
KD5
Query on KD5

Download SDF File 
Download CCD File 
B, C
4,7-anhydro-3-deoxy-D-manno-oct-2-ulosonic acid
C8 H12 O7
HVHHMEMCULPBED-UVSCYPECSA-N
 Ligand Interaction
GMH
Query on GMH

Download SDF File 
Download CCD File 
B, C
L-GLYCERO-D-MANNO-HEPTOPYRANOSE
C7 H14 O7
BGWQRWREUZVRGI-QQABCQGCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 55.350α = 90.00
b = 107.990β = 92.14
c = 55.650γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
CNSrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-27
    Type: Initial release
  • Version 1.1: 2016-03-23
    Type: Database references
  • Version 1.2: 2016-05-11
    Type: Database references