1R14

Carbohydrate recognition and neck domains of surfactant protein A (Sp-A) containing samarium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.247 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal structure of trimeric carbohydrate recognition and neck domains of surfactant protein A

Head, J.F.Mealy, T.R.McCormack, F.X.Seaton, B.A.

(2003) J Biol Chem 278: 43254-43260

  • DOI: https://doi.org/10.1074/jbc.M305628200
  • Primary Citation of Related Structures:  
    1R13, 1R14

  • PubMed Abstract: 

    Surfactant protein A (SP-A), one of four proteins associated with pulmonary surfactant, binds with high affinity to alveolar phospholipid membranes, positioning the protein at the first line of defense against inhaled pathogens. SP-A exhibits both calcium-dependent carbohydrate binding, a characteristic of the collectin family, and specific interactions with lipid membrane components. The crystal structure of the trimeric carbohydrate recognition domain and neck domain of SP-A was solved to 2.1-A resolution with multiwavelength anomalous dispersion phasing from samarium. Two metal binding sites were identified, one in the highly conserved lectin site and the other 8.5 A away. The interdomain carbohydrate recognition domain-neck angle is significantly less in SP-A than in the homologous collectins, surfactant protein D, and mannose-binding protein. This conformational difference may endow the SP-A trimer with a more extensive hydrophobic surface capable of binding lipophilic membrane components. The appearance of this surface suggests a putative binding region for membrane-derived SP-A ligands such as phosphatidylcholine and lipid A, the endotoxic lipid component of bacterial lipopolysaccharide that mediates the potentially lethal effects of Gram-negative bacterial infection.


  • Organizational Affiliation

    Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts 02118, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pulmonary surfactant-associated protein A148Rattus norvegicusMutation(s): 1 
Gene Names: SFTPA1 OR SFTPA OR SFTP1 OR SFTP-1
UniProt
Find proteins for P08427 (Rattus norvegicus)
Explore P08427 
Go to UniProtKB:  P08427
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08427
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.247 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.68α = 90
b = 97.68β = 90
c = 44.4γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-11-11
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-10-09
    Changes: Data collection, Structure summary