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


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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 of 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transport permease protein
A, C
296Staphylococcus aureusMutation(s): 0 
Gene Names: tagGSAUSA300_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:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Teichoic acids export ATP-binding protein TagH
B, D
264Staphylococcus aureusMutation(s): 0 
Gene Names: tagHSAUSA300_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