3I5W

Crystal structure of human alpha-defensin 5 (mutant R13H)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Selective arginines are important for the antibacterial activity and host cell interaction of human alpha-defensin 5

de Leeuw, E.Rajabi, M.Zou, G.Pazgier, M.Lu, W.

(2009) FEBS Lett 583: 2507-2512

  • DOI: https://doi.org/10.1016/j.febslet.2009.06.051
  • Primary Citation of Related Structures:  
    3I5W

  • PubMed Abstract: 

    Defensins constitute a major family of natural antimicrobial peptides that protect the host against microbial invasion. Here, we report on the antibacterial properties and cellular interaction of Human Defensin 5 as a function of its positive charge and hydrophobicity. We find that selective replacement of arginine residues in HD-5 by alanine or charge-neutral lysine residues reduces antibacterial killing as well as host cell interaction. We identify arginines at positions 9 and 28 in the HD-5 sequence as particularly important for its function. Replacement of arginine at position 13 to Histidine, as observed in a Crohn's disease patient, reduced bacterial killing strain-selectively. Finally, we find that HD-5 interacts with host cells via receptor-mediated mechanisms.


  • Organizational Affiliation

    University of Maryland Baltimore School of Medicine, Institute of Human Virology, Department of Biochemistry and Molecular Biology, Baltimore, MD 21201, USA. edeleeuw2@ihv.umaryland.edu


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Defensin-5
A, B
32Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for Q01523 (Homo sapiens)
Explore Q01523 
Go to UniProtKB:  Q01523
PHAROS:  Q01523
GTEx:  ENSG00000164816 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01523
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.018α = 90
b = 49.754β = 90
c = 62.355γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Derived calculations, Refinement description, Version format compliance
  • Version 1.2: 2012-04-11
    Changes: Derived calculations
  • Version 1.3: 2021-10-13
    Changes: Database references, Derived calculations
  • Version 1.4: 2021-10-27
    Changes: Source and taxonomy
  • Version 1.5: 2023-09-06
    Changes: Data collection, Refinement description