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Yorodumi- EMDB-12261: Structure of the HigB1 toxin mutant K95A from Mycobacterium tuber... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12261 | |||||||||
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Title | Structure of the HigB1 toxin mutant K95A from Mycobacterium tuberculosis (Rv1955) and its target, the cspA mRNA, on the E. coli Ribosome. | |||||||||
Map data | phenix sharpened map of the M. tuberculosis HigB1_K95A mutant toxin on the E. coli Ribosome. | |||||||||
Sample |
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Keywords | TOXIN | |||||||||
Function / homology | Function and homology information detoxification / negative regulation of growth / negative regulation of cytoplasmic translational initiation / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity ...detoxification / negative regulation of growth / negative regulation of cytoplasmic translational initiation / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / four-way junction DNA binding / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / RNA endonuclease activity / mRNA regulatory element binding translation repressor activity / ribosome assembly / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / regulation of DNA-templated transcription elongation / cytosolic ribosome assembly / DNA endonuclease activity / transcription antitermination / response to reactive oxygen species / translational initiation / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / large ribosomal subunit / ribosome biogenesis / small ribosomal subunit rRNA binding / ribosome binding / ribosomal large subunit assembly / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / molecular adaptor activity / Hydrolases; Acting on ester bonds / negative regulation of translation / response to hypoxia / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) / Mycobacterium tuberculosis (bacteria) / Escherichia coli (E. coli) / Mycobacterium tuberculosis H37Rv (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.11 Å | |||||||||
Authors | Giudice E / Mansour M | |||||||||
Funding support | France, Switzerland, 2 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Substrate recognition and cryo-EM structure of the ribosome-bound TAC toxin of Mycobacterium tuberculosis. Authors: Moise Mansour / Emmanuel Giudice / Xibing Xu / Hatice Akarsu / Patricia Bordes / Valérie Guillet / Donna-Joe Bigot / Nawel Slama / Gaetano D'urso / Sophie Chat / Peter Redder / Laurent ...Authors: Moise Mansour / Emmanuel Giudice / Xibing Xu / Hatice Akarsu / Patricia Bordes / Valérie Guillet / Donna-Joe Bigot / Nawel Slama / Gaetano D'urso / Sophie Chat / Peter Redder / Laurent Falquet / Lionel Mourey / Reynald Gillet / Pierre Genevaux / Abstract: Toxins of toxin-antitoxin systems use diverse mechanisms to control bacterial growth. Here, we focus on the deleterious toxin of the atypical tripartite toxin-antitoxin-chaperone (TAC) system of ...Toxins of toxin-antitoxin systems use diverse mechanisms to control bacterial growth. Here, we focus on the deleterious toxin of the atypical tripartite toxin-antitoxin-chaperone (TAC) system of Mycobacterium tuberculosis, whose inhibition requires the concerted action of the antitoxin and its dedicated SecB-like chaperone. We show that the TAC toxin is a bona fide ribonuclease and identify exact cleavage sites in mRNA targets on a transcriptome-wide scale in vivo. mRNA cleavage by the toxin occurs after the second nucleotide of the ribosomal A-site codon during translation, with a strong preference for CCA codons in vivo. Finally, we report the cryo-EM structure of the ribosome-bound TAC toxin in the presence of native M. tuberculosis cspA mRNA, revealing the specific mechanism by which the TAC toxin interacts with the ribosome and the tRNA in the P-site to cleave its mRNA target. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12261.map.gz | 458 MB | EMDB map data format | |
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Header (meta data) | emd-12261-v30.xml emd-12261.xml | 121.9 KB 121.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12261_fsc.xml | 18.2 KB | Display | FSC data file |
Images | emd_12261.png | 252.8 KB | ||
Masks | emd_12261_msk_1.map | 512 MB | Mask map | |
Filedesc metadata | emd-12261.cif.gz | 16.9 KB | ||
Others | emd_12261_additional_1.map.gz emd_12261_additional_10.map.gz emd_12261_additional_2.map.gz emd_12261_additional_3.map.gz emd_12261_additional_4.map.gz emd_12261_additional_5.map.gz emd_12261_additional_6.map.gz emd_12261_additional_7.map.gz emd_12261_additional_8.map.gz emd_12261_additional_9.map.gz emd_12261_half_map_1.map.gz emd_12261_half_map_2.map.gz | 390.8 MB 314.4 MB 406.4 MB 393.5 MB 393.5 MB 343.3 MB 345 MB 345 MB 311.1 MB 314.4 MB 410.2 MB 410.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12261 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12261 | HTTPS FTP |
-Validation report
Summary document | emd_12261_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_12261_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_12261_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | emd_12261_validation.cif.gz | 34.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12261 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12261 | HTTPS FTP |
-Related structure data
Related structure data | 7nbuMC 7awkC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12261.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | phenix sharpened map of the M. tuberculosis HigB1_K95A mutant toxin on the E. coli Ribosome. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.893 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
+Mask #1
+Additional map: Relion Multiboby full map of the E. Coli...
+Additional map: Relion Multiboby half map of the Head of...
+Additional map: Relion 3D refined full map of the M....
+Additional map: Relion Multiboby half map of the E. Coli...
+Additional map: Relion Multiboby half map of the E. Coli...
+Additional map: Relion Multiboby full map of the Body of...
+Additional map: Relion Multiboby half map of the Body of...
+Additional map: Relion Multiboby half map of the Body of...
+Additional map: Relion Multiboby full map of the Head of...
+Additional map: Relion Multiboby half map of the Head of...
+Half map: Relion half map of the M. tuberculosis HigB1 K95A...
+Half map: Relion half map of the M. tuberculosis HigB1 K95A...
-Sample components
+Entire : M. tuberculosis HigB1_K95A mutant toxin and its target, the CspA ...
+Supramolecule #1: M. tuberculosis HigB1_K95A mutant toxin and its target, the CspA ...
+Supramolecule #2: 30S Ribosomal subunit
+Supramolecule #3: 50S Ribosomal subunit
+Supramolecule #4: 16S rRNA
+Supramolecule #5: 30S ribosomal proteins
+Supramolecule #6: 23S and 5S rRNA
+Supramolecule #7: 50S ribosomal proteins
+Supramolecule #8: P-site fMet-tRNA(fMet)
+Supramolecule #9: E-site tRNA
+Supramolecule #10: cspA mRNA
+Supramolecule #11: HigB1 toxin
+Macromolecule #1: 16S ribosomal RNA
+Macromolecule #22: P-site fMet-tRNA(fMet)
+Macromolecule #23: E-site tRNA
+Macromolecule #24: cspA mRNA
+Macromolecule #26: 23S ribosomal RNA
+Macromolecule #27: 5S ribosomal RNA
+Macromolecule #2: 30S ribosomal protein S2
+Macromolecule #3: 30S ribosomal protein S3
+Macromolecule #4: 30S ribosomal protein S4
+Macromolecule #5: 30S ribosomal protein S5
+Macromolecule #6: 30S ribosomal protein S6
+Macromolecule #7: 30S ribosomal protein S7
+Macromolecule #8: 30S ribosomal protein S8
+Macromolecule #9: 30S ribosomal protein S9
+Macromolecule #10: 30S ribosomal protein S10
+Macromolecule #11: 30S ribosomal protein S11
+Macromolecule #12: 30S ribosomal protein S12
+Macromolecule #13: 30S ribosomal protein S13
+Macromolecule #14: 30S ribosomal protein S14
+Macromolecule #15: 30S ribosomal protein S15
+Macromolecule #16: 30S ribosomal protein S16
+Macromolecule #17: 30S ribosomal protein S17
+Macromolecule #18: 30S ribosomal protein S18
+Macromolecule #19: 30S ribosomal protein S19
+Macromolecule #20: 30S ribosomal protein S20
+Macromolecule #21: 30S ribosomal protein S21
+Macromolecule #25: Probable endoribonuclease HigB1
+Macromolecule #28: 50S ribosomal protein L2
+Macromolecule #29: 50S ribosomal protein L3
+Macromolecule #30: 50S ribosomal protein L4
+Macromolecule #31: 50S ribosomal protein L5
+Macromolecule #32: 50S ribosomal protein L6
+Macromolecule #33: 50S ribosomal protein L9
+Macromolecule #34: 50S ribosomal protein L13
+Macromolecule #35: 50S ribosomal protein L14
+Macromolecule #36: 50S ribosomal protein L15
+Macromolecule #37: 50S ribosomal protein L16,50S ribosomal protein L31
+Macromolecule #38: 50S ribosomal protein L16
+Macromolecule #39: 50S ribosomal protein L17
+Macromolecule #40: 50S ribosomal protein L18
+Macromolecule #41: 50S ribosomal protein L19
+Macromolecule #42: 50S ribosomal protein L20
+Macromolecule #43: 50S ribosomal protein L21
+Macromolecule #44: 50S ribosomal protein L22
+Macromolecule #45: 50S ribosomal protein L23
+Macromolecule #46: 50S ribosomal protein L24
+Macromolecule #47: 50S ribosomal protein L25
+Macromolecule #48: 50S ribosomal protein L27
+Macromolecule #49: 50S ribosomal protein L28
+Macromolecule #50: 50S ribosomal protein L29
+Macromolecule #51: 50S ribosomal protein L30
+Macromolecule #52: 50S ribosomal protein L32
+Macromolecule #53: 50S ribosomal protein L33
+Macromolecule #54: 50S ribosomal protein L34
+Macromolecule #55: 50S ribosomal protein L35
+Macromolecule #56: 50S ribosomal protein L36
+Macromolecule #57: MAGNESIUM ION
+Macromolecule #58: N-FORMYLMETHIONINE
+Macromolecule #59: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R3.5/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK III / Details: blot for 2s before plunging. |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Temperature | Min: 90.0 K / Max: 90.0 K |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 1-65 / Number grids imaged: 1 / Number real images: 6381 / Average exposure time: 6.5 sec. / Average electron dose: 52.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 30.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 120000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Details | Initial local fitting was done chain by chain using Chimera. The model was then refine using coot and phenix. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-7nbu: |