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Yorodumi- PDB-7zod: 70S E. coli ribosome with an extended uL23 loop from Candidatus m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zod | ||||||
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Title | 70S E. coli ribosome with an extended uL23 loop from Candidatus marinimicrobia | ||||||
Components |
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Keywords | RIBOSOME / exit tunnel / structural modification / ribosomal protein | ||||||
Function / homology | Function and homology information transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / ribosome assembly ...transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosome binding / ribosomal large subunit assembly / transferase activity / large ribosomal subunit rRNA binding / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.56 Å | ||||||
Authors | Mitropoulou, A. / Plessa, E. / Wlodarski, T. / Ahn, M. / Sidhu, H. / Becker, T.A. / Beckmann, R. / Cabrita, L.D. / Christodoulou, J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Modulating co-translational protein folding by rational design and ribosome engineering. Authors: Minkoo Ahn / Tomasz Włodarski / Alkistis Mitropoulou / Sammy H S Chan / Haneesh Sidhu / Elena Plessa / Thomas A Becker / Nediljko Budisa / Christopher A Waudby / Roland Beckmann / Anaïs M ...Authors: Minkoo Ahn / Tomasz Włodarski / Alkistis Mitropoulou / Sammy H S Chan / Haneesh Sidhu / Elena Plessa / Thomas A Becker / Nediljko Budisa / Christopher A Waudby / Roland Beckmann / Anaïs M E Cassaignau / Lisa D Cabrita / John Christodoulou / Abstract: Co-translational folding is a fundamental process for the efficient biosynthesis of nascent polypeptides that emerge through the ribosome exit tunnel. To understand how this process is modulated by ...Co-translational folding is a fundamental process for the efficient biosynthesis of nascent polypeptides that emerge through the ribosome exit tunnel. To understand how this process is modulated by the shape and surface of the narrow tunnel, we have rationally engineered three exit tunnel protein loops (uL22, uL23 and uL24) of the 70S ribosome by CRISPR/Cas9 gene editing, and studied the co-translational folding of an immunoglobulin-like filamin domain (FLN5). Our thermodynamics measurements employing F/N/methyl-TROSY NMR spectroscopy together with cryo-EM and molecular dynamics simulations reveal how the variations in the lengths of the loops present across species exert their distinct effects on the free energy of FLN5 folding. A concerted interplay of the uL23 and uL24 loops is sufficient to alter co-translational folding energetics, which we highlight by the opposite folding outcomes resulting from their extensions. These subtle modulations occur through a combination of the steric effects relating to the shape of the tunnel, the dynamic interactions between the ribosome surface and the unfolded nascent chain, and its altered exit pathway within the vestibule. These results illustrate the role of the exit tunnel structure in co-translational folding, and provide principles for how to remodel it to elicit a desired folding outcome. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zod.cif.gz | 2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7zod.ent.gz | 1.5 MB | Display | PDB format |
PDBx/mmJSON format | 7zod.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zod_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7zod_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7zod_validation.xml.gz | 107.8 KB | Display | |
Data in CIF | 7zod_validation.cif.gz | 180 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zo/7zod ftp://data.pdbj.org/pub/pdb/validation_reports/zo/7zod | HTTPS FTP |
-Related structure data
Related structure data | 14846MC 7z20C 7zp8C 7zq5C 7zq6C 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
+50S ribosomal protein ... , 28 types, 28 molecules 01234678cdefghjklmnopqrstuwy
-RNA chain , 3 types, 3 molecules abv
#9: RNA chain | Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: CP035706.1 |
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#10: RNA chain | Mass: 941620.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 2065591978 |
#29: RNA chain | Mass: 24846.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1847035720 |
-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: L23i empty ribosome / Type: RIBOSOME / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Source (recombinant) | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: 2500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 40.8 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING ONLY |
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3D reconstruction | Resolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 159764 / Symmetry type: POINT |