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Yorodumi- EMDB-43084: S. aureus TarL H300N in complex with CDP-ribitol (two tetramers w... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-43084 | |||||||||||||||
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Title | S. aureus TarL H300N in complex with CDP-ribitol (two tetramers with CHAPS micelle) | |||||||||||||||
Map data | Sharpened map | |||||||||||||||
Sample |
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Keywords | glycosyltransferase / 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 | |||||||||||||||
Biological species | Staphylococcus aureus (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||||||||
Authors | Li FKK / Strynadka NCJ / Worrall LJ | |||||||||||||||
Funding support | Canada, United States, 4 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_43084.map.gz | 56.9 MB | EMDB map data format | |
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Header (meta data) | emd-43084-v30.xml emd-43084.xml | 16.4 KB 16.4 KB | Display Display | EMDB header |
Images | emd_43084.png | 97.9 KB | ||
Masks | emd_43084_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-43084.cif.gz | 5.4 KB | ||
Others | emd_43084_half_map_1.map.gz emd_43084_half_map_2.map.gz | 58.8 MB 58.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43084 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43084 | HTTPS FTP |
-Related structure data
Related structure data | 8v33C 8v34C 8va1C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_43084.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.32375 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_43084_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_43084_half_map_1.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A
File | emd_43084_half_map_2.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : S. aureus TarL H300N with CDP-ribitol and CHAPS
Entire | Name: S. aureus TarL H300N with CDP-ribitol and CHAPS |
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Components |
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-Supramolecule #1: S. aureus TarL H300N with CDP-ribitol and CHAPS
Supramolecule | Name: S. aureus TarL H300N with CDP-ribitol and CHAPS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Two tetramers with CHAPS micelle |
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Source (natural) | Organism: Staphylococcus aureus (bacteria) |
-Macromolecule #1: TarL H300N
Macromolecule | Name: TarL H300N / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Staphylococcus aureus (bacteria) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MVKSKIYIDK IYWERVQLFV EGHSENLDL EDSNFVLRNL T ETRTMKAN DVKIDGNQFV CR FNVAILD NGYYLPEDKY LLV NEQELD YIAQLNPDVI NDAY QNLKP EQEEEYNELE TQNGK INFL LQTYLKEFRK GGISKK TVY TVTPEISSDV NEFVLDV VV ...String: MVKSKIYIDK IYWERVQLFV EGHSENLDL EDSNFVLRNL T ETRTMKAN DVKIDGNQFV CR FNVAILD NGYYLPEDKY LLV NEQELD YIAQLNPDVI NDAY QNLKP EQEEEYNELE TQNGK INFL LQTYLKEFRK GGISKK TVY TVTPEISSDV NEFVLDV VV TTPEVKSIYI VRKYKELR K YFRKQSFNTR QFIFKAIFN TTKFFHLKKG NTVLFTSDSR PTMSGNFEY IYNEMLRQNL D KKYDIHTV FKANITDRRG II DKFRLPY LLGKADYIFV DDF HPLIYT VRFRRSQEVI QVWN AVGAF KTVGFSRTGK KGGPF IDSL NHRSYTKAYV SSETDI PFY AEAFGIKEKN VVPTGVP RT DVLFDEAYAT QIKQEMED E LPIIKGKKVI LFAPTFRGS GHGTAHYPFF KIDFERLARY CEKNNAVVL FKMHPFVKNR L NIADKHKQ YFVDVSDFRE VN DILFITD LLISDYSSLI YEY AVFKKP MIFYAFDLED YITT RDFYE PYESFVPGKI VQSFD ALMD ALDNEDYEGE KVIPFL DKH FKYQDGRSSE RLVRNLF GS KLVPRGSAAA ALEHHHHH H HH UniProtKB: Teichoic acid ribitol-phosphate polymerase TarL |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 9.3 mg/mL | ||||||||
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Buffer | pH: 7.5 Component:
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Grid | Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR | ||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated 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 recording | Film 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 |
-Image processing
Startup model | Type of model: NONE |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |
Final reconstruction | Applied symmetry - Point group: D4 (2x4 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1341400 |