9Q2Q | pdb_00009q2q

Nucleotide-free structure of PmtCD in peptidisc


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Cryo-EM analysis of the Staphylococcus aureus phenol-soluble modulin exporter PmtCD apo form in detergent micelles, nanodiscs and peptidiscs.

Hu, J.Lazarski, A.C.Li, F.K.K.Worrall, L.J.Burgin, D.J.Zeytuni, N.Dickey, S.W.Otto, M.Strynadka, N.C.J.

(2025) Commun Biol 8: 1576-1576

  • DOI: https://doi.org/10.1038/s42003-025-08955-3
  • Primary Citation of Related Structures:  
    9Q1Y, 9Q2N, 9Q2Q, 9Q2R

  • PubMed Abstract: 

    Staphylococci secrete amphipathic peptides known as phenol soluble modulins (PSMs) that play a variety of pathogenic roles including host cell membrane destruction, biofilm development, and the triggering of inflammatory responses. PSM export is facilitated by the essential ATP-binding cassette (ABC) transporter PmtCD, which also provides producer immunity toward the membrane-damaging PSMs. Here, we report cryo-EM structures of PmtCD in a nucleotide-free state using different membrane mimetics - detergent, nanodisc and peptidisc - all featuring the transmembrane domains in an open state with a remarkably expansive intervening lumen. The consistently sized lumen suggests the possibility for two α-helical amphipathic PSMs to pack and passage within. A continuous hydrophobic surface with no apparent single high affinity site is in keeping with the ability of PmtCD to export a variety of hydrophobic PSM peptide substrates. The ATP driven collapse of the PmtD lumen is consistent with the lateral access and extrusion mechanisms of related ABC transporters that translocate membrane embedded substrates. Along with a new ADP product complex and prior ATPγS-bound form, these structures provide insights into the export of PSMs and a foundation for design of trojan horse antimicrobials that target MRSA strains from within by blocking membranolytic PSM export.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, Canada.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phenol-soluble modulin export ABC transporter permease subunit PmtDA,
C [auth B]
249Staphylococcus aureusMutation(s): 0 
Gene Names: D7S40_12560
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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ABC transporter ATP-binding proteinB [auth C],
D
290Staphylococcus aureusMutation(s): 0 
Gene Names: 
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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-26
    Type: Initial release