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- EMDB-43083: S. aureus TarL H300N in complex with CDP-ribitol (single tetramer) -

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Basic information

Entry
Database: EMDB / ID: EMD-43083
TitleS. aureus TarL H300N in complex with CDP-ribitol (single tetramer)
Map dataSharpened map
Sample
  • Complex: S. aureus TarL H300N with CDP-ribitol and CHAPS
    • Protein or peptide: Teichoic acid ribitol-phosphate polymerase TarL
  • Ligand: CDP-ribitol
Keywordsglycosyltransferase / polymerase / monotopic / amphipathic / TRANSFERASE
Function / homology
Function and homology information


CDP-ribitol ribitolphosphotransferase / CDP-ribitol ribitolphosphotransferase activity / CDP-glycerol glycerophosphotransferase activity / teichoic acid biosynthetic process / cell wall organization / plasma membrane
Similarity search - Function
: / CDP-glycerol glycerophosphotransferase / CDP-glycerol glycerophosphotransferase, C-terminal domain / CDP-glycerol glycerophosphotransferase, N-terminal domain / CDP-Glycerol:Poly(glycerophosphate) glycerophosphotransferase
Similarity search - Domain/homology
Teichoic acid ribitol-phosphate polymerase TarL
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLi FKK / Worrall LJ / Strynadka NCJ
Funding support Canada, United States, 4 items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
Canadian Institutes of Health Research (CIHR) Canada
Howard Hughes Medical Institute (HHMI) United States
Canada Research Chairs Canada
CitationJournal: Sci Adv / Year: 2024
Title: Cryo-EM analysis of TarL, a polymerase in wall teichoic acid biogenesis central to virulence and antibiotic resistance.
Authors: Franco K K Li / Liam J Worrall / Robert T Gale / Eric D Brown / Natalie C J Strynadka /
Abstract: Wall teichoic acid (WTA), a covalent adduct of Gram-positive bacterial cell wall peptidoglycan, contributes directly to virulence and antibiotic resistance in pathogenic species. Polymerization of ...Wall teichoic acid (WTA), a covalent adduct of Gram-positive bacterial cell wall peptidoglycan, contributes directly to virulence and antibiotic resistance in pathogenic species. Polymerization of the WTA ribitol-phosphate chain is catalyzed by TarL, a member of the largely uncharacterized TagF-like family of membrane-associated enzymes. We report the cryo-electron microscopy structure of TarL, showing a tetramer that forms an extensive membrane-binding platform of monotopic helices. TarL is composed of an amino-terminal immunoglobulin-like domain and a carboxyl-terminal glycosyltransferase-B domain for ribitol-phosphate polymerization. The active site of the latter is complexed to donor substrate cytidine diphosphate-ribitol, providing mechanistic insights into the catalyzed phosphotransfer reaction. Furthermore, the active site is surrounded by electropositive residues that serve to retain the lipid-linked acceptor for polymerization. Our data advance general insight into the architecture and membrane association of the still poorly characterized monotopic membrane protein class and present molecular details of ribitol-phosphate polymerization that may aid in the design of new antimicrobials.
History
DepositionDec 10, 2023-
Header (metadata) releaseApr 3, 2024-
Map releaseApr 3, 2024-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43083.png

Downloads & links

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Map

FileDownload / File: emd_43083.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Voxel sizeX=Y=Z: 1.32375 Å
Density
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.001874645 - 2.74805
Average (Standard dev.)0.001134579 (±0.024991136)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 338.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_43083_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_43083_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_43083_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : S. aureus TarL H300N with CDP-ribitol and CHAPS

EntireName: S. aureus TarL H300N with CDP-ribitol and CHAPS
Components
  • Complex: S. aureus TarL H300N with CDP-ribitol and CHAPS
    • Protein or peptide: Teichoic acid ribitol-phosphate polymerase TarL
  • Ligand: CDP-ribitol

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Supramolecule #1: S. aureus TarL H300N with CDP-ribitol and CHAPS

SupramoleculeName: S. aureus TarL H300N with CDP-ribitol and CHAPS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Staphylococcus aureus (bacteria)

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Macromolecule #1: Teichoic acid ribitol-phosphate polymerase TarL

MacromoleculeName: Teichoic acid ribitol-phosphate polymerase TarL / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: CDP-ribitol ribitolphosphotransferase
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 68.510703 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MVKSKIYIDK IYWERVQLFV EGHSENLDLE DSNFVLRNLT ETRTMKANDV KIDGNQFVCR FNVAILDNGY YLPEDKYLLV NEQELDYIA QLNPDVINDA YQNLKPEQEE EYNELETQNG KINFLLQTYL KEFRKGGISK KTVYTVTPEI SSDVNEFVLD V VVTTPEVK ...String:
MVKSKIYIDK IYWERVQLFV EGHSENLDLE DSNFVLRNLT ETRTMKANDV KIDGNQFVCR FNVAILDNGY YLPEDKYLLV NEQELDYIA QLNPDVINDA YQNLKPEQEE EYNELETQNG KINFLLQTYL KEFRKGGISK KTVYTVTPEI SSDVNEFVLD V VVTTPEVK SIYIVRKYKE LRKYFRKQSF NTRQFIFKAI FNTTKFFHLK KGNTVLFTSD SRPTMSGNFE YIYNEMLRQN LD KKYDIHT VFKANITDRR GIIDKFRLPY LLGKADYIFV DDFHPLIYTV RFRRSQEVIQ VWNAVGAFKT VGFSRTGKKG GPF IDSLNH RSYTKAYVSS ETDIPFYAEA FGIKEKNVVP TGVPRTDVLF DEAYATQIKQ EMEDELPIIK GKKVILFAPT FRGS GHGTA HYPFFKIDFE RLARYCEKNN AVVLFKMHPF VKNRLNIADK HKQYFVDVSD FREVNDILFI TDLLISDYSS LIYEY AVFK KPMIFYAFDL EDYITTRDFY EPYESFVPGK IVQSFDALMD ALDNEDYEGE KVIPFLDKHF KYQDGRSSER LVRNLF GSK LVPRGSAAAA LEHHHHHHHH

UniProtKB: Teichoic acid ribitol-phosphate polymerase TarL

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Macromolecule #2: CDP-ribitol

MacromoleculeName: CDP-ribitol / type: ligand / ID: 2 / Number of copies: 4 / Formula: V2V
Molecular weightTheoretical: 537.307 Da
Chemical component information

ChemComp-V2V:
CDP-ribitol

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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

Concentration9.3 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
20.0 mMHEPES
500.0 mMSodium chloride
6.5 mMCHAPS
GridMaterial: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 81000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 19380 / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 190753

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Atomic model buiding 1

Initial modelPDB ID:

3l7l


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-8va1:
S. aureus TarL H300N in complex with CDP-ribitol (single tetramer)

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