1PW9

High resolution crystal structure of an active recombinant fragment of human lung surfactant protein D


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 509-523

  • Primary Citation of Related Structures:  1PWB
  • Also Cited By: 3IKN, 3IKP, 3IKQ, 3IKR, 4E52

  • PubMed Abstract: 
  • Lung surfactant protein D (SP-D) can directly interact with carbohydrate residues on pulmonary pathogens and allergens, stimulate immune cells, and manipulate cytokine and chemokine profiles during the immune response in the lungs. Therapeutic admini ...

    Lung surfactant protein D (SP-D) can directly interact with carbohydrate residues on pulmonary pathogens and allergens, stimulate immune cells, and manipulate cytokine and chemokine profiles during the immune response in the lungs. Therapeutic administration of rfhSP-D, a recombinant homotrimeric fragment of human SP-D comprising the alpha-helical coiled-coil neck plus three CRDs, protects mice against lung allergy and infection caused by the fungal pathogen Aspergillus fumigatus. The high resolution crystal structures of maltose-bound rfhSP-D to 1.4A, and of rfhSP-D to 1.6A, define the fine detail of the mode and nature of carbohydrate recognition and provide insights into how a small fragment of human SP-D can bind to allergens/antigens or whole pathogens, and at the same time recruit and engage effector cells and molecules of humoral immunity. A previously unreported calcium ion, located on the trimeric axis in a pore at the bottom of the funnel formed by the three CRDs and close to the neck-CRD interface, is coordinated by a triad of glutamate residues which are, to some extent, neutralised by their interactions with a triad of exposed lysine residues in the funnel. The spatial relationship between the neck and the CRDs is maintained internally by these lysine residues, and externally by a glutamine, which forms a pair of hydrogen-bonds within an external cleft at each neck-CRD interface. Structural links between the central pore and the cleft suggest a possible effector mechanism for immune cell surface receptor binding in the presence of bound, extended natural lipopolysaccharide and phospholipid ligands. The structural requirements for such an effector mechanism, involving both the trimeric framework for multivalent ligand binding and recognition sites formed from more than one subunit, are present in both native hSP-D and rfhSP-D, providing a possible explanation for the significant biological activity of rfhSP-D.


    Related Citations: 
    • Crystal structure of the trimeric alpha-helical coiled-coil and the three lectin domains of human lung surfactant protein D
      Hakansson, K.,Lim, N.K.,Hoppe, H.J.,Reid, K.B.
      (1999) Structure 7: 255


    Organizational Affiliation

    School of Life Sciences, Keele University, Staffordshire ST5 5BG, Keele, UK. a.k.shrive@keele.ac.uk




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 1 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.227 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 55.550α = 90.00
b = 108.520β = 91.20
c = 55.690γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
SCALAdata scaling
X-PLORrefinement
X-PLORmodel building
MOSFLMdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-08-05
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance