6XJI | pdb_00006xji

PmtCD ABC exporter at C1 symmetry


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6XJI

This is version 1.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 128.07 kDa 
  • Atom Count: 8,754 
  • Modeled Residue Count: 1,082 
  • Deposited Residue Count: 1,112 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Phenol-soluble modulin export ABC transporter permease subunit PmtD
A, B
266Staphylococcus aureusMutation(s): 0 
Gene Names: D7S40_12560
Membrane Entity: Yes 
UniProt
Find proteins for Q2FWX0 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FWX0 
Go to UniProtKB:  Q2FWX0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FWX0
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ABC transporter ATP-binding protein
C, D
290Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for X5EJW5 (Staphylococcus aureus)
Explore X5EJW5 
Go to UniProtKB:  X5EJW5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupX5EJW5
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3

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: 2024-03-06
    Changes: Data collection, Database references
  • Version 1.2: 2025-05-28
    Changes: Data collection, Structure summary