2YMK

Crystal structure of the hexameric anti-microbial peptide channel dermcidin

  • Classification: ANTIBIOTIC
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2012-10-09 Released: 2012-10-17 
  • Deposition Author(s): Zeth, K.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal Structure and Functional Mechanism of a Human Antimicrobial Membrane Channel.

Song, C.Weichbrodt, C.Salnikov, E.S.Dynowski, M.Forsberg, B.O.Bechinger, B.Steinem, C.De Groot, B.L.Zachariae, U.Zeth, K.

(2013) Proc Natl Acad Sci U S A 110: 4586

  • DOI: 10.1073/pnas.1214739110
  • Primary Citation of Related Structures:  
    2YMK

  • PubMed Abstract: 
  • Multicellular organisms fight bacterial and fungal infections by producing peptide-derived broad-spectrum antibiotics. These host-defense peptides compromise the integrity of microbial cell membranes and thus evade pathways by which bacteria develop ...

    Multicellular organisms fight bacterial and fungal infections by producing peptide-derived broad-spectrum antibiotics. These host-defense peptides compromise the integrity of microbial cell membranes and thus evade pathways by which bacteria develop rapid antibiotic resistance. Although more than 1,700 host-defense peptides have been identified, the structural and mechanistic basis of their action remains speculative. This impedes the desired rational development of these agents into next-generation antibiotics. We present the X-ray crystal structure as well as solid-state NMR spectroscopy, electrophysiology, and MD simulations of human dermcidin in membranes that reveal the antibiotic mechanism of this major human antimicrobial, found to suppress Staphylococcus aureus growth on the epidermal surface. Dermcidin forms an architecture of high-conductance transmembrane channels, composed of zinc-connected trimers of antiparallel helix pairs. Molecular dynamics simulations elucidate the unusual membrane permeation pathway for ions and show adjustment of the pore to various membranes. Our study unravels the comprehensive mechanism for the membrane-disruptive action of this mammalian host-defense peptide at atomistic level. The results may form a foundation for the structure-based design of peptide antibiotics.


    Organizational Affiliation

    Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DCD-1A, B, C48Homo sapiensMutation(s): 0 
Gene Names: DCDAIDDDSEP
EC: 3.4
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Adventitious Membrane Proteins: Alpha-helical Pore-forming Toxins.
Protein: 
Dermicidin hexameric anti-microbial peptide channel
Find proteins for P81605 (Homo sapiens)
Explore P81605 
Go to UniProtKB:  P81605
NIH Common Fund Data Resources
PHAROS  P81605
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.354α = 90
b = 50.724β = 117.74
c = 45.738γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
DMphasing
BUCCANEERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2012-10-09 
  • Released Date: 2012-10-17 
  • Deposition Author(s): Zeth, K.

Revision History 

  • Version 1.0: 2012-10-17
    Type: Initial release
  • Version 1.1: 2013-03-06
    Changes: Database references, Other
  • Version 1.2: 2013-04-03
    Changes: Database references
  • Version 1.3: 2013-12-25
    Changes: Database references, Structure summary