6XFU | pdb_00006xfu

PmtCD peptide exporter basket domain

• PDB DOI: https://doi.org/10.2210/pdb6XFU/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2020-06-16 Released: 2020-10-14 
• Deposition Author(s): Zeytuni, N., Strynadka, N.C.J., Alexander, J.A.N.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.194 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

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

• PubMed: 32998902 
• 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.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology and the Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada.
Pathogen Molecular Genetics Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
CryoEM Shared Resources, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
High Resolution Macromolecular Cryo-Electron Microscopy facility, University of British Columbia, Vancouver, V6T 1Z3, BC, Canada.
Department of Biochemistry and Molecular Biology and the Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada. [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 16.45 kDa 
• Atom Count: 1,360 
• Modeled Residue Count: 139 
• Deposited Residue Count: 140 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter ATP-binding protein	A, B	70	Staphylococcus aureus	Mutation(s): 0  Gene Names:  ybhF_2, pmtC, ybhF_1, ybhF_3, BN1321_320024, BTN44_02050, C7P97_04805, CSC83_02360, CSC87_13000, EP54_10395, EQ90_13985, ER624_12880, ERS072840_01916, HMPREF3211_02244, NCTC10654_02103, NCTC13131_01274, NCTC7878_02640, NCTC7988_02070, RK64_10625
UniProt
Find proteins for Q2FWW9 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FWW9  Go to UniProtKB:  Q2FWW9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SCN (Subject of Investigation/LOI)	C [auth A], D [auth B]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.194 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.462	α = 90
b = 45.375	β = 90
c = 73.82	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-10-14 
Deposition Author(s): Zeytuni, N., Strynadka, N.C.J., Alexander, J.A.N.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	Operating grant

Revision History  

• Version 1.0: 2020-10-14
  Type: Initial release
  
• Version 1.1: 2023-04-05
  Changes: Database references
• Version 1.2: 2023-10-25
  Changes: Data collection, Refinement description