6U2D

PmtCD peptide exporter basket domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insight into the Staphylococcus aureus ATP-driven exporter of virulent peptide toxins

Zeytuni, N.Dickey, S.W.Hu, J.Chou, H.T.Worrall, L.J.Alexander, J.A.N.Carlson, M.L.Nosella, M.Duong, F.Yu, Z.Otto, M.Strynadka, N.C.J.

(2020) Sci Adv 6: eabb8219

  • DOI: https://doi.org/10.1126/sciadv.abb8219
  • Primary Citation of Related Structures:  
    6U2D, 6XFU, 6XJH, 6XJI

  • PubMed Abstract: 

    Staphylococcus aureus is a major human pathogen that has acquired alarming broad-spectrum antibiotic resistance. One group of secreted toxins with key roles during infection is the phenol-soluble modulins (PSMs). PSMs are amphipathic, membrane-destructive cytolytic peptides that are exported to the host-cell environment by a designated adenosine 5'-triphosphate (ATP)-binding cassette (ABC) transporter, the PSM transporter (PmtABCD). Here, we demonstrate that the minimal Pmt unit necessary for PSM export is PmtCD and provide its first atomic characterization by single-particle cryo-EM and x-ray crystallography. We have captured the transporter in the ATP-bound state at near atomic resolution, revealing a type II ABC exporter fold, with an additional cytosolic domain. Comparison to a lower-resolution nucleotide-free map displaying an "open" conformation and putative hydrophobic inner chamber of a size able to accommodate the binding of two PSM peptides provides mechanistic insight and sets the foundation for therapeutic design.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology and the Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ABC transporter ATP-binding protein
A, B, C, D
66Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for Q2FWW9 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FWW9 
Go to UniProtKB:  Q2FWW9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FWW9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
I [auth B]
K [auth C]
L [auth C]
F [auth A],
G [auth A],
I [auth B],
K [auth C],
L [auth C],
M [auth C],
N [auth C]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
J [auth C],
O [auth D],
P [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.214 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.19α = 90
b = 39.783β = 108.94
c = 56.499γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaOperating grant

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-14
    Type: Initial release
  • Version 1.1: 2024-03-13
    Changes: Data collection, Database references, Refinement description