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Yorodumi- PDB-6h4n: Structure of a hibernating 100S ribosome reveals an inactive conf... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6h4n | |||||||||
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Title | Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1 - 70S 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: 3 Å | |||||||||
Authors | Beckert, B. / Turk, M. / Czech, A. / Berninghausen, O. / Beckmann, R. / Ignatova, Z. / Plitzko, J. / Wilson, N.D. | |||||||||
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 | 6h4n.cif.gz | 3.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6h4n.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6h4n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6h4n_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6h4n_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6h4n_validation.xml.gz | 213.8 KB | Display | |
Data in CIF | 6h4n_validation.cif.gz | 377 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h4/6h4n ftp://data.pdbj.org/pub/pdb/validation_reports/h4/6h4n | HTTPS FTP |
-Related structure data
Related structure data | 0137MC 0139C 6h58C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 5 types, 5 molecules aABwI
#1: RNA chain | Mass: 497197.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: GenBank: 1359176725 |
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#22: RNA chain | Mass: 941305.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: GenBank: 1036415628 |
#23: RNA chain | Mass: 38813.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: GenBank: 1393501787 |
#53: RNA chain | Mass: 24771.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: GenBank: 1063812051 |
#57: RNA chain | Mass: 1482.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) |
+30S ribosomal protein ... , 21 types, 21 molecules bcdefghijklmnopqrstuy
+50S ribosomal protein ... , 29 types, 29 molecules CDEFGHJKLMNOPQRSTUVWXYZ012346
-Protein , 2 types, 2 molecules vx
#54: Protein | Mass: 6520.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0AFW2 |
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#56: Protein | Mass: 10768.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0AFX0 |
-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: 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 and 7.9 resolution, respectively. ...Details: 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 and 7.9 resolution, respectively. The structures reveal the binding sites for HPF and RMF as well as the unexpected presence of deacylated E-site tRNA and ribosomal protein bS1. HPF interacts with the anticodon-stem-loop of the E-tRNA and occludes the binding site for the mRNA 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. Entity ID: all / Source: NATURAL |
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Molecular weight | Units: MEGADALTONS / Experimental value: NO |
Source (natural) | Organism: Escherichia coli BW25113 (bacteria) |
Buffer solution | pH: 7.5 Details: B100S buffer (25 mM Hepes pH 7.5, 100 mM KOAc, 15 mM Mg(OAc)2, 1 mM dithiothreitol) |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK III / 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 |
Image recording | Electron dose: 2.5 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 188304 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT |