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Yorodumi- PDB-6h58: Structure of a hibernating 100S ribosome reveals an inactive conf... -
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-Basic information
Entry | Database: PDB / ID: 6h58 | |||||||||
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Title | Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1 - Full 100S Hibernating E. coli Ribosome | |||||||||
Components |
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Keywords | RIBOSOME / 100S / cryo-EM / E-site tRNA / hibernation / HPF / RMF / S1 | |||||||||
Function / homology | Function and homology information negative regulation of translation in response to stress / dormancy process / negative regulation of translational elongation / RNA secondary structure unwinding / positive regulation of cytoplasmic translation / negative regulation of cytoplasmic translational initiation / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing ...negative regulation of translation in response to stress / dormancy process / negative regulation of translational elongation / RNA secondary structure unwinding / positive regulation of cytoplasmic translation / negative regulation of cytoplasmic translational initiation / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / ribosomal small subunit binding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / four-way junction DNA binding / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / ribosome assembly / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / regulation of DNA-templated transcription elongation / cytosolic ribosome assembly / DNA endonuclease activity / transcription antitermination / response to reactive oxygen species / translational initiation / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / large ribosomal subunit / ribosome biogenesis / small ribosomal subunit rRNA binding / ribosome binding / ribosomal large subunit assembly / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / molecular adaptor activity / single-stranded RNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli BW25113 (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.9 Å | |||||||||
Authors | Beckert, B. / Turk, M. / Czech, A. / Berninghausen, O. / Beckmann, R. / Ignatova, Z. / Plitzko, J. / Wilson, D.N. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Nat Microbiol / Year: 2018 Title: Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1. Authors: Bertrand Beckert / Martin Turk / Andreas Czech / Otto Berninghausen / Roland Beckmann / Zoya Ignatova / Jürgen M Plitzko / Daniel N Wilson / Abstract: To survive under conditions of stress, such as nutrient deprivation, bacterial 70S ribosomes dimerize to form hibernating 100S particles. In γ-proteobacteria, such as Escherichia coli, 100S ...To survive under conditions of stress, such as nutrient deprivation, bacterial 70S ribosomes dimerize to form hibernating 100S particles. In γ-proteobacteria, such as Escherichia coli, 100S formation requires the ribosome modulation factor (RMF) and the hibernation promoting factor (HPF). Here we present single-particle cryo-electron microscopy structures of hibernating 70S and 100S particles isolated from stationary-phase E. coli cells at 3.0 Å and 7.9 Å resolution, respectively. The structures reveal the binding sites for HPF and RMF as well as the unexpected presence of deacylated E-site transfer RNA and ribosomal protein bS1. HPF interacts with the anticodon-stem-loop of the E-tRNA and occludes the binding site for the messenger RNA as well as A- and P-site tRNAs. RMF facilitates stabilization of a compact conformation of bS1, which together sequester the anti-Shine-Dalgarno sequence of the 16S ribosomal RNA (rRNA), thereby inhibiting translation initiation. At the dimerization interface, the C-terminus of uS2 probes the mRNA entrance channel of the symmetry-related particle, thus suggesting that dimerization inactivates ribosomes by blocking the binding of mRNA within the channel. The back-to-back E. coli 100S arrangement is distinct from 100S particles observed previously in Gram-positive bacteria, and reveals a unique role for bS1 in translation regulation. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6h58.cif.gz | 6.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6h58.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6h58.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6h58_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6h58_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6h58_validation.xml.gz | 407.1 KB | Display | |
Data in CIF | 6h58_validation.cif.gz | 726.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/6h58 ftp://data.pdbj.org/pub/pdb/validation_reports/h5/6h58 | HTTPS FTP |
-Related structure data
Related structure data | 0139MC 0137C 6h4nC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+50S ribosomal protein ... , 29 types, 58 molecules 000111222333444666CCCDDDEEEFFFGGGHHHJJJKKKLLL...
-RNA chain , 4 types, 8 molecules AAABBBaaawww
#7: RNA chain | Mass: 941305.250 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: GenBank: 1036415628 #8: RNA chain | Mass: 38813.133 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: GenBank: 1393501787 #32: RNA chain | Mass: 498725.406 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: GenBank: 1359176725 #56: RNA chain | Mass: 24771.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: GenBank: 1063812051 |
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+30S ribosomal protein ... , 21 types, 42 molecules bbbcccdddeeefffggghhhiiijjjkkklllmmmnnnoooppp...
-Protein , 2 types, 4 molecules vvvxxx
#53: Protein | Mass: 6520.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0AFW2 #54: Protein | Mass: 10768.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0AFX0 |
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-Details
Has protein modification | Y |
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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: Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1 Type: RIBOSOME Details: single particle cryo-electron microscopy structures of hibernating 100S particles isolated from stationary phase E. coli cells Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Escherichia coli BW25113 (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/1 |
Vitrification | Cryogen name: ETHANE-PROPANE |
-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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 1.15 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | |||||||||||||||||||||
3D reconstruction | Resolution: 7.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18000 / Symmetry type: POINT | |||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | |||||||||||||||||||||
Atomic model building | PDB-ID: 6H4N Accession code: 6H4N / Source name: PDB / Type: experimental model |