[English] 日本語
![](img/lk-miru.gif)
- PDB-7nbu: Structure of the HigB1 toxin mutant K95A from Mycobacterium tuber... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7nbu | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the HigB1 toxin mutant K95A from Mycobacterium tuberculosis (Rv1955) and its target, the cspA mRNA, on the E. coli Ribosome. | |||||||||
![]() |
| |||||||||
![]() | TOXIN | |||||||||
Function / homology | ![]() 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 / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / DNA endonuclease activity / ribosomal large subunit assembly / 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 / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / molecular adaptor activity / Hydrolases; Acting on ester bonds / response to hypoxia / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.11 Å | |||||||||
![]() | Giudice, E. / Mansour, M. / Chat, S. / D'Urso, G. / Gillet, R. / Genevaux, P. | |||||||||
Funding support | ![]() ![]()
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 3.2 MB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 222.5 KB | Display | |
Data in CIF | ![]() | 380.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 12261MC ![]() 7awkC C: citing same article ( M: map data used to model this data |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
-RNA chain , 6 types, 6 molecules AVWXab
#1: RNA chain | Mass: 498846.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GB U000096.3 545778205 223771-225312 / Source: (natural) ![]() ![]() |
---|---|
#22: RNA chain | Mass: 24818.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#23: RNA chain | Mass: 589.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#24: RNA chain | Mass: 3144.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: rv3648c (cspA) Source: (natural) ![]() |
#26: RNA chain | Mass: 941822.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GB U000096.3 545778205 225759 - 228662 / Source: (natural) ![]() ![]() |
#27: RNA chain | Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GB U000096.3 545778205 228756 - 228875 / Source: (natural) ![]() ![]() |
-30S ribosomal protein ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTU
#2: Protein | Mass: 24971.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7V0 / Source: (natural) ![]() ![]() |
---|---|
#3: Protein | Mass: 23078.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7V3 / Source: (natural) ![]() ![]() |
#4: Protein | Mass: 23383.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7V8 / Source: (natural) ![]() ![]() |
#5: Protein | Mass: 16475.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7W1 / Source: (natural) ![]() ![]() |
#6: Protein | Mass: 11996.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P02358 / Source: (natural) ![]() ![]() |
#7: Protein | Mass: 17162.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P02359 / Source: (natural) ![]() ![]() |
#8: Protein | Mass: 14015.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7W7 / Source: (natural) ![]() ![]() |
#9: Protein | Mass: 14554.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7X3 / Source: (natural) ![]() ![]() |
#10: Protein | Mass: 11196.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7R5 / Source: (natural) ![]() ![]() |
#11: Protein | Mass: 12488.185 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7R9 / Source: (natural) ![]() ![]() |
#12: Protein | Mass: 13683.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7S3 / Source: (natural) ![]() ![]() |
#13: Protein | Mass: 12738.911 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7S9 / Source: (natural) ![]() ![]() |
#14: Protein | Mass: 11475.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0AG59 / Source: (natural) ![]() ![]() |
#15: Protein | Mass: 10159.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0ADZ4 / Source: (natural) ![]() ![]() |
#16: Protein | Mass: 9136.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7T3 / Source: (natural) ![]() ![]() |
#17: Protein | Mass: 9164.815 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0AG63 / Source: (natural) ![]() ![]() |
#18: Protein | Mass: 7735.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7T7 / Source: (natural) ![]() ![]() |
#19: Protein | Mass: 9492.095 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7U3 / Source: (natural) ![]() ![]() |
#20: Protein | Mass: 9577.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P0A7U7 / Source: (natural) ![]() ![]() |
#21: Protein | Mass: 8392.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P68679 / Source: (natural) ![]() ![]() |
-Protein , 1 types, 1 molecules Y
#25: Protein | Mass: 14003.255 Da / Num. of mol.: 1 / Mutation: K95A Source method: isolated from a genetically manipulated source Details: P9WJA5 Source: (gene. exp.) ![]() Strain: ATCC 25618 / H37Rv / Gene: higB1, higB, Rv1955 / Plasmid: pET20b / Production host: ![]() ![]() References: UniProt: P9WJA5, Hydrolases; Acting on ester bonds |
---|
+50S ribosomal protein ... , 29 types, 29 molecules cdefghijklZmnopqrstuvwxyz0123
-Non-polymers , 3 types, 316 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/FME.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/FME.gif)
![](data/chem/img/ZN.gif)
#57: Chemical | ChemComp-MG / #58: Chemical | ChemComp-FME / | #59: Chemical | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Source (natural) |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Buffer component |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R3.5/1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295.15 K / Details: blot for 2s before plunging |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 120000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm / C2 aperture diameter: 30 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 90 K / Temperature (min): 90 K |
Image recording | Average exposure time: 6.5 sec. / Electron dose: 52 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6381 |
Image scans | Width: 3710 / Height: 3838 / Movie frames/image: 65 / Used frames/image: 1-65 |
-
Processing
EM software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 294820 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13877 / Num. of class averages: 1 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL Details: Initial local fitting was done chain by chain using Chimera. The model was then refine using coot and phenix. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7K00 Accession code: 7K00 / Source name: PDB / Type: experimental model | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 94.15 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|