6CS9

Crystal structure of human beta-defensin 2 in complex with PIP2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Human beta-defensin 2 killsCandida albicansthrough phosphatidylinositol 4,5-bisphosphate-mediated membrane permeabilization.

Jarva, M.Phan, T.K.Lay, F.T.Caria, S.Kvansakul, M.Hulett, M.D.

(2018) Sci Adv 4: eaat0979-eaat0979

  • DOI: 10.1126/sciadv.aat0979
  • Primary Citation of Related Structures:  
    6CS9

  • PubMed Abstract: 
  • Human defensins belong to a subfamily of the cationic antimicrobial peptides and act as a first line of defense against invading microbes. Their often broad-spectrum antimicrobial and antitumor activities make them attractive for therapeutic development; however, their precise molecular mechanism(s) of action remains to be defined ...

    Human defensins belong to a subfamily of the cationic antimicrobial peptides and act as a first line of defense against invading microbes. Their often broad-spectrum antimicrobial and antitumor activities make them attractive for therapeutic development; however, their precise molecular mechanism(s) of action remains to be defined. We show that human β-defensin 2 (HBD-2) permeabilizes Candida albicans cell membranes via a mechanism targeting the plasma membrane lipid phosphatidylinositol 4,5-bisphosphate (PIP 2 ). We determined the structure of HBD-2 bound to PIP 2 , which revealed two distinct PIP 2 -binding sites, and showed, using functional assays, that mutations in these sites ablate PIP 2 -mediated fungal growth inhibition by HBD-2. Our study provides the first insight into lipid-mediated human defensin membrane permeabilization at an atomic level and reveals a unique mode of lipid engagement to permeabilize cell membranes.


    Organizational Affiliation

    Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-defensin 4AA, B41Homo sapiensMutation(s): 0 
Gene Names: DEFB4ADEFB102DEFB2DEFB4DEFB4B
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O15263 (Homo sapiens)
Explore O15263 
Go to UniProtKB:  O15263
PHAROS:  O15263
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PIO
Query on PIO

Download Ideal Coordinates CCD File 
C [auth A], D [auth B][(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
C25 H49 O19 P3
XLNCEHRXXWQMPK-MJUMVPIBSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PIOIC50:  2200   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: P 1 21 1
  • Diffraction Data DOI: 10.15785/SBGRID/568 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.871α = 90
b = 25.538β = 98.64
c = 40.17γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaFT130101349

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-25
    Type: Initial release
  • Version 1.1: 2018-08-08
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence