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- EMDB-45554: Cryo-EM structure of S. aureus TarGH in complex with AMP-PNP and ... -

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Basic information

Entry
Database: EMDB / ID: EMD-45554
TitleCryo-EM structure of S. aureus TarGH in complex with AMP-PNP and targocil-II
Map dataRefined sharpened map
Sample
  • Complex: TarGH
    • Protein or peptide: Transport permease protein
    • Protein or peptide: Teichoic acids export ATP-binding protein TagH
  • Ligand: Targocil-II
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: water
KeywordsABC transporter / teichoic acid / bacteria / MEMBRANE PROTEIN
Function / homology
Function and homology information


ABC-type teichoic-acid transporter / ABC-type teichoic acid transporter activity / lipopolysaccharide transport / ABC-type transporter activity / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Teichoic acids export ATP-binding protein tagH. / ABC transporter, teichoic acids export TagH-like / : / : / ABC transporter integral membrane type-2 domain profile. / ABC-2 type transporter / ABC-2 type transporter / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...Teichoic acids export ATP-binding protein tagH. / ABC transporter, teichoic acids export TagH-like / : / : / ABC transporter integral membrane type-2 domain profile. / ABC-2 type transporter / ABC-2 type transporter / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Transport permease protein / Teichoic acids export ATP-binding protein TagH
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsPeters SC / Worrall LJ / Strynadka NCJ
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Nat Commun / Year: 2025
Title: Cryo-EM analyses unveil details of mechanism and targocil-II mediated inhibition of S. aureus WTA transporter TarGH.
Authors: Franco K K Li / Shaun C Peters / Liam J Worrall / Tianjun Sun / Jinhong Hu / Marija Vuckovic / Maya Farha / Armando Palacios / Nathanael A Caveney / Eric D Brown / Natalie C J Strynadka /
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 ...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.
History
DepositionJun 27, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45554.png

Downloads & links

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Map

FileDownload / File: emd_45554.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRefined sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.18 Å/pix.
x 250 pix.
= 295. Å		1.18 Å/pix.
x 250 pix.
= 295. Å		1.18 Å/pix.
x 250 pix.
= 295. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.18 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.783518 - 1.0552558
Average (Standard dev.)0.0003966657 (±0.021361107)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 295.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map

Fileemd_45554_half_map_1.map
AnnotationHalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map

Fileemd_45554_half_map_2.map
AnnotationHalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TarGH

EntireName: TarGH
Components
  • Complex: TarGH
    • Protein or peptide: Transport permease protein
    • Protein or peptide: Teichoic acids export ATP-binding protein TagH
  • Ligand: Targocil-II
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: TarGH

SupramoleculeName: TarGH / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: Hetero tetramer TarG2H2
Source (natural)Organism: Staphylococcus aureus (bacteria)

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Macromolecule #1: Transport permease protein

MacromoleculeName: Transport permease protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 34.240527 KDa
Recombinant expressionOrganism: Lactococcus lactis (lactic acid bacteria)
SequenceString: MGSSHHHHHH HHHHSSGLVP RGSHMSAIGT VFKEHVKNFY LIQRLAQFQV KIINHSNYLG VAWELINPVM QIMVYWMVFG LGIRSNAPI HGVPFVYWLL VGISMWFFIN QGILEGTKAI TQKFNQVSKM NFPLSIIPTY IVTSRFYGHL GLLLLVIIAC M FTGIYPSI ...String:
MGSSHHHHHH HHHHSSGLVP RGSHMSAIGT VFKEHVKNFY LIQRLAQFQV KIINHSNYLG VAWELINPVM QIMVYWMVFG LGIRSNAPI HGVPFVYWLL VGISMWFFIN QGILEGTKAI TQKFNQVSKM NFPLSIIPTY IVTSRFYGHL GLLLLVIIAC M FTGIYPSI HIIQLLIYVP FCFFLTASVT LLTSTLGVLV RDTQMLMQAI LRILFYFSPI LWLPKNHGIS GLIHEMMKYN PV YFIAESY RAAILYHEWY FMDHWKLMLY NFGIVAIFFA IGAYLHMKYR DQFADFL

UniProtKB: Transport permease protein

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Macromolecule #2: Teichoic acids export ATP-binding protein TagH

MacromoleculeName: Teichoic acids export ATP-binding protein TagH / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: ABC-type teichoic-acid transporter
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 29.806553 KDa
Recombinant expressionOrganism: Lactococcus lactis (lactic acid bacteria)
SequenceString: MNVSVNIKNV TKEYRIYRTN KERMKDALIP KHKNKTFFAL DDISLKAYEG DVIGLVGING SGKSTLSNII GGSLSPTVGK VDRNGEVSV IAISAGLSGQ LTGIENIEFK MLCMGFKRKE IKAMTPKIIE FSELGEFIYQ PVKKYSSGMR AKLGFSINIT V NPDILVID ...String:
MNVSVNIKNV TKEYRIYRTN KERMKDALIP KHKNKTFFAL DDISLKAYEG DVIGLVGING SGKSTLSNII GGSLSPTVGK VDRNGEVSV IAISAGLSGQ LTGIENIEFK MLCMGFKRKE IKAMTPKIIE FSELGEFIYQ PVKKYSSGMR AKLGFSINIT V NPDILVID EALSVGDQTF AQKCLDKIYE FKEQNKTIFF VSHNLGQVRQ FCTKIAWIEG GKLKDYGELD DVLPKYEAFL ND FKKKSKA EQKEFRNKLD ESRFVIK

UniProtKB: Teichoic acids export ATP-binding protein TagH

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Macromolecule #3: Targocil-II

MacromoleculeName: Targocil-II / type: ligand / ID: 3 / Number of copies: 2 / Formula: A1AV9
Molecular weightTheoretical: 479.909 Da

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Macromolecule #4: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 4 / Number of copies: 2 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 6 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6jbh

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 117415
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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