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Yorodumi- PDB-7oqh: CryoEM structure of the transcription termination factor Rho from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7oqh | |||||||||
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Title | CryoEM structure of the transcription termination factor Rho from Mycobacterium tuberculosis | |||||||||
Components | Transcription termination factor Rho | |||||||||
Keywords | TRANSCRIPTION / transcription termination factor / RNA helicase / ATP-dependent / molecular motor | |||||||||
Function / homology | Function and homology information ATP-dependent activity, acting on RNA / helicase activity / DNA-templated transcription termination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / hydrolase activity / RNA binding / ATP binding Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.32 Å | |||||||||
Authors | Saridakis, E. / Vishwakarma, R. / Lai Kee Him, J. / Martin, K. / Simon, I. / Cohen-Gonsaud, M. / Coste, F. / Bron, P. / Margeat, E. / Boudvillain, M. | |||||||||
Funding support | France, 2items
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Citation | Journal: Commun Biol / Year: 2022 Title: Cryo-EM structure of transcription termination factor Rho from Mycobacterium tuberculosis reveals bicyclomycin resistance mechanism. Authors: Emmanuel Saridakis / Rishi Vishwakarma / Josephine Lai-Kee-Him / Kevin Martin / Isabelle Simon / Martin Cohen-Gonsaud / Franck Coste / Patrick Bron / Emmanuel Margeat / Marc Boudvillain / Abstract: The bacterial Rho factor is a ring-shaped motor triggering genome-wide transcription termination and R-loop dissociation. Rho is essential in many species, including in Mycobacterium tuberculosis ...The bacterial Rho factor is a ring-shaped motor triggering genome-wide transcription termination and R-loop dissociation. Rho is essential in many species, including in Mycobacterium tuberculosis where rho gene inactivation leads to rapid death. Yet, the M. tuberculosis Rho [Rho] factor displays poor NTPase and helicase activities, and resistance to the natural Rho inhibitor bicyclomycin [BCM] that remain unexplained. To address these issues, we solved the cryo-EM structure of Rho at 3.3 Å resolution. The Rho hexamer is poised into a pre-catalytic, open-ring state wherein specific contacts stabilize ATP in intersubunit ATPase pockets, thereby explaining the cofactor preference of Rho. We reveal a leucine-to-methionine substitution that creates a steric bulk in BCM binding cavities near the positions of ATP γ-phosphates, and confers resistance to BCM at the expense of motor efficiency. Our work contributes to explain the unusual features of Rho and provides a framework for future antibiotic development. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7oqh.cif.gz | 398.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7oqh.ent.gz | 308.8 KB | Display | PDB format |
PDBx/mmJSON format | 7oqh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7oqh_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7oqh_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7oqh_validation.xml.gz | 70.6 KB | Display | |
Data in CIF | 7oqh_validation.cif.gz | 104.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/7oqh ftp://data.pdbj.org/pub/pdb/validation_reports/oq/7oqh | HTTPS FTP |
-Related structure data
Related structure data | 12701MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 67362.703 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Production host: Escherichia coli (E. coli) References: UniProt: A0A045J3H4, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement #2: Chemical | ChemComp-ATP / #3: Chemical | ChemComp-MG / Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Transcription termination factor Rho from Mycrobacterium Tuberculosis Type: COMPLEX Details: The cryo-EM sample was prepared by mixing M tuberculosis Rho (0.6mg mL-1, as per nano-drop, A280) with 10uM dC20 oligonucleotide and 1mM ATP in a buffer (10mM Tris-HCl 150mM 5mM MgCl2 pH 7.6) ...Details: The cryo-EM sample was prepared by mixing M tuberculosis Rho (0.6mg mL-1, as per nano-drop, A280) with 10uM dC20 oligonucleotide and 1mM ATP in a buffer (10mM Tris-HCl 150mM 5mM MgCl2 pH 7.6) by incubating 10min at 22 oC Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) | Organism: Mycobacterium tuberculosis (bacteria) | ||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: BL21 / Cell: Rosetta-DE3 / Plasmid: pET28b | ||||||||||||||||||||||||
Buffer solution | pH: 7.9 | ||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: PELCO Ultrathin Carbon with Lacey Carbon | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: NITROGEN / Humidity: 22 % / Chamber temperature: 295.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Calibrated magnification: 165000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 48 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 10888 |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2217252 | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 986385 / Num. of class averages: 2 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 1PV4 Accession code: 1PV4 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.54 Å2 | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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