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 9CFL | pdb_00009cfl

Cryo-EM structure of S. aureus TarGH in complex with ATP-gamma-S


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9CFL

This is version 1.0 of the entry. See complete history. 

Literature

Cryo-EM analyses unveil details of mechanism and targocil-II mediated inhibition of S. aureus WTA transporter TarGH.

Li, F.K.K., Peters, S.C., Worrall, L.J., Sun, T., Hu, J., Vuckovic, M., Farha, M., Palacios, A., Caveney, N.A., Brown, E.D., Strynadka, N.C.J.

(2025) Nat Commun 16: 3224-3224

  • DOI: https://doi.org/10.1038/s41467-025-58202-w
  • Primary Citation Related Structures: 
    9CFL, 9CFP, 9MHD, 9MHU, 9MHZ

  • PubMed Abstract: 

    Wall teichoic acid (WTA) is a polyol phosphate polymer that covalently decorates peptidoglycan of gram-positive bacteria, including Staphylococcus aureus. Central to WTA biosynthesis is flipping of lipid-linked precursors across the cell membrane by TarGH, a type V ABC transporter. Here, we present cryo-EM structures of S. aureus TarGH in the presence of targocil-II, a promising small-molecule lead with β-lactam antibiotic synergistic action. Targocil-II binds to the extracellular dimerisation interface of TarG, we suggest mimicking flipped but not yet released substrate. In absence of targocil-II and in complex with ATP analogue ATPγS, determined at 2.3 Å resolution, the ATPase active site is allosterically inhibited. This is due to a so far undescribed D-loop conformation, potentially minimizing spurious ATP hydrolysis in the absence of substrate. Targocil-II binding comparatively causes local and remote conformational changes through to the TarH active site, with the D-loop now optimal for ATP hydrolysis. These structures suggest an ability to modulate ATP hydrolysis in a WTA substrate dependent manner and a jammed ATPase cycle as the basis of the observed inhibition by targocil-II. The molecular insights provide an unprecedented basis for development of TarGH targeted therapeutics for treatment of multidrug-resistant S. aureus and other gram-positive bacterial infections.


  • 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: 132.33 kDa 
  • Atom Count: 8,925 
  • Modeled Residue Count: 1,068 
  • Deposited Residue Count: 1,120 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transport permease protein
A, C
296Staphylococcus aureusMutation(s): 0 
Gene Names: tagG, SAUSA300_0625
Membrane Entity: Yes 
UniProt
Find proteins for A0A0H2XIF1 (Staphylococcus aureus (strain USA300))
Explore A0A0H2XIF1 
Go to UniProtKB:  A0A0H2XIF1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2XIF1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Teichoic acids export ATP-binding protein TagH
B, D
264Staphylococcus aureusMutation(s): 0 
Gene Names: tagH, SAUSA300_0624
EC: 7.5.2.4
Membrane Entity: Yes 
UniProt
Find proteins for Q2FJ01 (Staphylococcus aureus (strain USA300))
Explore Q2FJ01 
Go to UniProtKB:  Q2FJ01
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FJ01
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AV0
(Subject of Investigation/LOI)

Query on AV0



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
I [auth C]
Lauryl Maltose Neopentyl Glycol
C47 H88 O22
MADJBYLAYPCCOO-VWHTXWAPSA-N
AGS
(Subject of Investigation/LOI)

Query on AGS



Download:Ideal Coordinates CCD File
G [auth B],
J [auth D]
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
H [auth B],
K [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

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: 2025-04-23
    Type: Initial release