5I7K

Crystal Structure of Human SPLUNC1 Dolphin Mutant D1 (G58A, S61A, G62E, G63D, G66D, I67T)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.218 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural Features Essential to the Antimicrobial Functions of Human SPLUNC1.

Walton, W.G.Ahmad, S.Little, M.S.Kim, C.S.Tyrrell, J.Lin, Q.Di, Y.P.Tarran, R.Redinbo, M.R.

(2016) Biochemistry 55: 2979-2991

  • DOI: https://doi.org/10.1021/acs.biochem.6b00271
  • Primary Citation of Related Structures:  
    5I7J, 5I7K, 5I7L

  • PubMed Abstract: 

    SPLUNC1 is an abundantly secreted innate immune protein in the mammalian respiratory tract that exerts bacteriostatic and antibiofilm effects, binds to lipopolysaccharide (LPS), and acts as a fluid-spreading surfactant. Here, we unravel the structural elements essential for the surfactant and antimicrobial functions of human SPLUNC1 (short palate lung nasal epithelial clone 1). A unique α-helix (α4) that extends from the body of SPLUNC1 is required for the bacteriostatic, surfactant, and LPS binding activities of this protein. Indeed, we find that mutation of just four leucine residues within this helical motif to alanine is sufficient to significantly inhibit the fluid spreading abilities of SPLUNC1, as well as its bacteriostatic actions against Gram-negative pathogens Burkholderia cenocepacia and Pseudomonas aeruginosa. Conformational flexibility in the body of SPLUNC1 is also involved in the bacteriostatic, surfactant, and LPS binding functions of the protein as revealed by disulfide mutants introduced into SPLUNC1. In addition, SPLUNC1 exerts antibiofilm effects against Gram-negative bacteria, although α4 is not involved in this activity. Interestingly, though, the introduction of surface electrostatic mutations away from α4 based on the unique dolphin SPLUNC1 sequence, and confirmed by crystal structure, is shown to impart antibiofilm activity against Staphylococcus aureus, the first SPLUNC1-dependent effect against a Gram-positive bacterium reported to date. Together, these data pinpoint SPLUNC1 structural motifs required for the antimicrobial and surfactant actions of this protective human protein.


  • Organizational Affiliation

    Departments of Chemistry, Biochemistry, and Microbiology, University of North Carolina , 4350 Genome Sciences Building, Chapel Hill, North Carolina 27599-3290, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BPI fold-containing family A member 1
A, B
240Homo sapiensMutation(s): 6 
Gene Names: BPIFA1LUNXNASGPLUNCSPLUNC1SPURTUNQ787/PRO1606
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NP55 (Homo sapiens)
Explore Q9NP55 
Go to UniProtKB:  Q9NP55
PHAROS:  Q9NP55
GTEx:  ENSG00000198183 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NP55
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.218 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.027α = 90
b = 204.927β = 90
c = 118.652γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR01 HL108927

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2016-06-08
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Refinement description