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Yorodumi- PDB-7zp8: 70S E. coli ribosome with a stalled filamin domain 5 nascent chain -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zp8 | ||||||
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Title | 70S E. coli ribosome with a stalled filamin domain 5 nascent chain | ||||||
Components |
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Keywords | RIBOSOME / exit tunnel / structural modification / ribosomal protein / folded nascent chain | ||||||
Function / homology | Function and homology information regulation of pseudopodium assembly / anterior cell cortex / Cell-extracellular matrix interactions / pseudopodium assembly / ISG15 antiviral mechanism / Platelet degranulation / sorocarp development / posterior cell cortex / chemotaxis to cAMP / lateral cell cortex ...regulation of pseudopodium assembly / anterior cell cortex / Cell-extracellular matrix interactions / pseudopodium assembly / ISG15 antiviral mechanism / Platelet degranulation / sorocarp development / posterior cell cortex / chemotaxis to cAMP / lateral cell cortex / phototaxis / macropinocytic cup / RHO GTPases activate PAKs / protein kinase B binding / actin crosslink formation / thermotaxis / hyperosmotic response / mitogen-activated protein kinase binding / lamellipodium assembly / cortical actin cytoskeleton / cell leading edge / pseudopodium / phagocytic cup / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / phagocytosis / DnaA-L2 complex / translation repressor activity / response to cAMP / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / extracellular matrix / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit assembly / response to reactive oxygen species / cell motility / DNA-templated transcription termination / response to radiation / small GTPase binding / mRNA 5'-UTR binding / actin filament binding / large ribosomal subunit / cell migration / cell cortex / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / actin cytoskeleton organization / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Dictyostelium discoideum (eukaryote) Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å | ||||||
Authors | Mitropoulou, A. / Plessa, E. / Wlodarski, T. / Ahn, M. / Chan, S.H.S. / 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 | 7zp8.cif.gz | 2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7zp8.ent.gz | 1.5 MB | Display | PDB format |
PDBx/mmJSON format | 7zp8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zp8_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7zp8_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7zp8_validation.xml.gz | 108.3 KB | Display | |
Data in CIF | 7zp8_validation.cif.gz | 176.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/7zp8 ftp://data.pdbj.org/pub/pdb/validation_reports/zp/7zp8 | HTTPS FTP |
-Related structure data
Related structure data | 14850MC 7z20C 7zodC 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 |
#31: 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 |
-Protein , 1 types, 1 molecules z
#32: Protein | Mass: 16122.779 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: abpC, DDB_G0269100 / Production host: Escherichia coli (E. coli) / References: UniProt: P13466 |
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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: Ribosomal nascent chain of FLN5 / 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 / Humidity: 95 % / Chamber temperature: 277 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 defocus max: 2400 nm / Nominal defocus min: 1200 nm |
Image recording | Average exposure time: 3 sec. / Electron dose: 14.45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18_3845: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 614463 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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