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Yorodumi- PDB-8uua: Cryo-EM structure of the Listeria innocua 50S ribosomal subunit i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8uua | |||||||||||||||
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Title | Cryo-EM structure of the Listeria innocua 50S ribosomal subunit in complex with HflXr (structure III) | |||||||||||||||
Components |
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Keywords | RIBOSOME / cryo-EM / recycling / HflXr / time-resolved | |||||||||||||||
Function / homology | Function and homology information large ribosomal subunit / ribosome binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation ...large ribosomal subunit / ribosome binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / GTPase activity / mRNA binding / GTP binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Listeria monocytogenes serovar 1/2a (bacteria) Listeria innocua (bacteria) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||||||||
Authors | Seely, S.M. / Basu, R.S. / Gagnon, M.G. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Nucleic Acids Res / Year: 2024 Title: Mechanistic insights into the alternative ribosome recycling by HflXr. Authors: Savannah M Seely / Ritwika S Basu / Matthieu G Gagnon / Abstract: During stress conditions such as heat shock and antibiotic exposure, ribosomes stall on messenger RNAs, leading to inhibition of protein synthesis. To remobilize ribosomes, bacteria use rescue ...During stress conditions such as heat shock and antibiotic exposure, ribosomes stall on messenger RNAs, leading to inhibition of protein synthesis. To remobilize ribosomes, bacteria use rescue factors such as HflXr, a homolog of the conserved housekeeping GTPase HflX that catalyzes the dissociation of translationally inactive ribosomes into individual subunits. Here we use time-resolved cryo-electron microscopy to elucidate the mechanism of ribosome recycling by Listeria monocytogenes HflXr. Within the 70S ribosome, HflXr displaces helix H69 of the 50S subunit and induces long-range movements of the platform domain of the 30S subunit, disrupting inter-subunit bridges B2b, B2c, B4, B7a and B7b. Our findings unveil a unique ribosome recycling strategy by HflXr which is distinct from that mediated by RRF and EF-G. The resemblance between HflXr and housekeeping HflX suggests that the alternative ribosome recycling mechanism reported here is universal in the prokaryotic kingdom. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8uua.cif.gz | 2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8uua.ent.gz | 1.5 MB | Display | PDB format |
PDBx/mmJSON format | 8uua.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8uua_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8uua_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8uua_validation.xml.gz | 139.9 KB | Display | |
Data in CIF | 8uua_validation.cif.gz | 244.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uu/8uua ftp://data.pdbj.org/pub/pdb/validation_reports/uu/8uua | HTTPS FTP |
-Related structure data
Related structure data | 42577MC 8uu4C 8uu5C 8uu6C 8uu7C 8uu8C 8uu9C 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
-Protein , 1 types, 1 molecules v
#1: Protein | Mass: 47610.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria) Strain: ATCC BAA-679 / EGD-e / References: UniProt: Q8Y8Y0 |
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-RNA chain , 2 types, 2 molecules AB
#2: RNA chain | Mass: 951061.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: GenBank: 2288068686 |
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#3: RNA chain | Mass: 37304.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / Strain: ATCC33090 / References: GenBank: 1774324476 |
+Large ribosomal subunit protein ... , 27 types, 27 molecules CDEFGLMNOPQRSTUVWYZ12345678
-Non-polymers , 5 types, 339 molecules
#31: Chemical | ChemComp-GCP / | ||||||
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#32: Chemical | ChemComp-MG / #33: Chemical | ChemComp-K / | #34: Chemical | #35: Water | ChemComp-HOH / | |
-Details
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: Listeria innocua 50S ribosomal subunit bound to HflXr / Type: RIBOSOME / Entity ID: #1-#19, #21-#30 / Source: NATURAL |
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Molecular weight | Value: 1.5 MDa / Experimental value: NO |
Source (natural) | Organism: Listeria innocua (bacteria) |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 295 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 96000 X / Nominal defocus max: 2300 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10446 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 332513 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7NHN Accession code: 7NHN / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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