+Open data
-Basic information
Entry | Database: PDB / ID: 8cgl | ||||||
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Title | Cryo-EM structure of RNase J from Helicobacter pylori | ||||||
Components | Ribonuclease J | ||||||
Keywords | RNA BINDING PROTEIN / ribonuclease / RNase J / degradosome / Helicobacter pylori | ||||||
Function / homology | Function and homology information 5'-3' RNA exonuclease activity / RNA endonuclease activity / regulation of cell growth / mRNA processing / rRNA processing / protein homotetramerization / Hydrolases; Acting on ester bonds / protein homodimerization activity / RNA binding / zinc ion binding ...5'-3' RNA exonuclease activity / RNA endonuclease activity / regulation of cell growth / mRNA processing / rRNA processing / protein homotetramerization / Hydrolases; Acting on ester bonds / protein homodimerization activity / RNA binding / zinc ion binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Helicobacter pylori B128 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||
Authors | Lulla, A. / Luisi, B.F. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Acetylation regulates the oligomerization state and activity of RNase J, the Helicobacter pylori major ribonuclease. Authors: Alejandro Tejada-Arranz / Aleksei Lulla / Maxime Bouilloux-Lafont / Evelyne Turlin / Xue-Yuan Pei / Thibaut Douché / Mariette Matondo / Allison H Williams / Bertrand Raynal / Ben F Luisi / Hilde De Reuse / Abstract: In the gastric pathogen Helicobacter pylori, post-transcriptional regulation relies strongly on the activity of the essential ribonuclease RNase J. Here, we elucidated the crystal and cryo-EM ...In the gastric pathogen Helicobacter pylori, post-transcriptional regulation relies strongly on the activity of the essential ribonuclease RNase J. Here, we elucidated the crystal and cryo-EM structures of RNase J and determined that it assembles into dimers and tetramers in vitro. We found that RNase J extracted from H. pylori is acetylated on multiple lysine residues. Alanine substitution of several of these residues impacts on H. pylori morphology, and thus on RNase J function in vivo. Mutations of Lysine 649 modulates RNase J oligomerization in vitro, which in turn influences ribonuclease activity in vitro. Our structural analyses of RNase J reveal loops that gate access to the active site and rationalizes how acetylation state of K649 can influence activity. We propose acetylation as a regulatory level controlling the activity of RNase J and its potential cooperation with other enzymes of RNA metabolism in H. pylori. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cgl.cif.gz | 505.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cgl.ent.gz | 382.9 KB | Display | PDB format |
PDBx/mmJSON format | 8cgl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cgl_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8cgl_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8cgl_validation.xml.gz | 60.1 KB | Display | |
Data in CIF | 8cgl_validation.cif.gz | 95.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cg/8cgl ftp://data.pdbj.org/pub/pdb/validation_reports/cg/8cgl | HTTPS FTP |
-Related structure data
Related structure data | 16647MC 7pcrC 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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-Components
#1: Protein | Mass: 79196.930 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori B128 (bacteria) / Gene: rnaJ, HPB128_16g80 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 References: UniProt: B9XZG7, Hydrolases; Acting on ester bonds |
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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: Helicobacter pylori RNase J / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.316 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Helicobacter pylori (bacteria) / Strain: B128 | ||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: C43(DE3) / Plasmid: pExp-xMBP-TEV-HP_RNJ-CHis | ||||||||||||||||||||
Buffer solution | pH: 7.2 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm / Calibrated defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Image recording | Electron dose: 40.58 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34061 / Symmetry type: POINT |