+Open data
-Basic information
Entry | Database: PDB / ID: 8q3p | |||||||||
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Title | Bacterial transcription termination factor Rho G150D mutant | |||||||||
Components | Transcription termination factor Rho | |||||||||
Keywords | TRANSCRIPTION / Rho / termination | |||||||||
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 / ATP hydrolysis activity / RNA binding / ATP binding / identical protein binding / membrane / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Said, N. / Hilal, T. / Wahl, M.C. | |||||||||
Funding support | Germany, 1items
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Citation | Journal: bioRxiv / Year: 2023 Title: Transcription termination factor ρ polymerizes under stress. Authors: Bing Wang / Nelly Said / Tarek Hilal / Mark Finazzo / Markus C Wahl / Irina Artsimovitch / Abstract: Bacterial RNA helicase ρ is a genome sentinel that terminates synthesis of damaged and junk RNAs that are not translated by the ribosome. Co-transcriptional RNA surveillance by ρ is essential for ...Bacterial RNA helicase ρ is a genome sentinel that terminates synthesis of damaged and junk RNAs that are not translated by the ribosome. Co-transcriptional RNA surveillance by ρ is essential for quality control of the transcriptome during optimal growth. However, it is unclear how bacteria protect their RNAs from overzealous ρ during dormancy or stress, conditions common in natural habitats. Here we used cryogenic electron microscopy, biochemical, and genetic approaches to show that residue substitutions, ADP, or ppGpp promote hyper-oligomerization of ρ. Our results demonstrate that nucleotides bound at subunit interfaces control ρ switching from active hexamers to inactive higher-order oligomers and extended filaments. Polymers formed upon exposure to antibiotics or ppGpp disassemble when stress is relieved, thereby directly linking termination activity to cellular physiology. Inactivation of ρ through hyper-oligomerization is a regulatory strategy shared by RNA polymerases, ribosomes, and metabolic enzymes across all life. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8q3p.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8q3p.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 8q3p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8q3p_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 8q3p_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 8q3p_validation.xml.gz | 183.3 KB | Display | |
Data in CIF | 8q3p_validation.cif.gz | 275.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/8q3p ftp://data.pdbj.org/pub/pdb/validation_reports/q3/8q3p | HTTPS FTP |
-Related structure data
Related structure data | 18132MC 8q3nC 8q3oC 8q3qC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 48616.809 Da / Num. of mol.: 18 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia (bacteria) / Gene: rho, nitA, psuA, rnsC, sbaA, tsu, b3783, JW3756 / Production host: Escherichia coli (E. coli) References: UniProt: P0AG30, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement #2: Chemical | ChemComp-ADP / #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: helical reconstruction |
-Sample preparation
Component | Name: Filament of Rho mutant G150D / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.6 |
Specimen | Conc.: 2.4 mg/ml / 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 R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 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 / Nominal defocus max: 2000 nm / Nominal defocus min: 900 nm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 40.57 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2511 |
-Processing
EM software | Name: PHENIX / Version: 1.20_4459: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 54.26 ° / Axial rise/subunit: 10.76 Å / Axial symmetry: C1 | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 495704 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 140359 / Algorithm: BACK PROJECTION / Symmetry type: HELICAL | ||||||||||||||||||||||||
Atomic model building | B value: 96.4 / Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||
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