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Yorodumi- PDB-8w8d: Structural mechanism of inhibition of the Rho transcription termi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8w8d | ||||||
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Title | Structural mechanism of inhibition of the Rho transcription termination factor by Rof | ||||||
Components |
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Keywords | TRANSCRIPTION / Escherichia coli Rho-Rof complex / Rho-dependent termination / antitermination | ||||||
Function / homology | Function and homology information regulation of termination of DNA-templated transcription / ATP-dependent activity, acting on RNA / transcription antitermination / 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 / membrane ...regulation of termination of DNA-templated transcription / ATP-dependent activity, acting on RNA / transcription antitermination / 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 / membrane / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
Authors | Zhang, J. / Wang, C. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: A widely conserved protein Rof inhibits transcription termination factor Rho and promotes Salmonella virulence program. Authors: Jing Zhang / Shuo Zhang / Wei Zhou / Xiang Zhang / Guanjin Li / Ruoxuan Li / Xingyu Lin / Ziying Chen / Fang Liu / Pan Shen / Xiaogen Zhou / Yue Gao / Zhenguo Chen / Yanjie Chao / Chengyuan Wang / Abstract: Transcription is crucial for the expression of genetic information and its efficient and accurate termination is required for all living organisms. Rho-dependent termination could rapidly terminate ...Transcription is crucial for the expression of genetic information and its efficient and accurate termination is required for all living organisms. Rho-dependent termination could rapidly terminate unwanted premature RNAs and play important roles in bacterial adaptation to changing environments. Although Rho has been discovered for about five decades, the regulation mechanisms of Rho-dependent termination are still not fully elucidated. Here we report that Rof is a conserved antiterminator and determine the cryogenic electron microscopy structure of Rho-Rof antitermination complex. Rof binds to the open-ring Rho hexamer and inhibits the initiation of Rho-dependent termination. Rof's N-terminal α-helix undergoes conformational changes upon binding with Rho, and is key in facilitating Rof-Rho interactions. Rof binds to Rho's primary binding site (PBS) and excludes Rho from binding with PBS ligand RNA at the initiation step. Further in vivo analyses in Salmonella Typhimurium show that Rof is required for virulence gene expression and host cell invasion, unveiling a physiological function of Rof and transcription termination in bacterial pathogenesis. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8w8d.cif.gz | 488.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8w8d.ent.gz | 410.5 KB | Display | PDB format |
PDBx/mmJSON format | 8w8d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/8w8d ftp://data.pdbj.org/pub/pdb/validation_reports/w8/8w8d | HTTPS FTP |
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-Related structure data
Related structure data | 37342MC 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: 47070.168 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (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: Protein | Mass: 9490.628 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Gene: rof, yaeO, b0189, JW0184 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AFW8 #3: Water | ChemComp-HOH / | |
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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: Rho-Rof antitermination complex / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
-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 FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 47 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.20.1_4487: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1099028 / Symmetry type: POINT | ||||||||||||||||||||||||
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