+Open data
-Basic information
Entry | Database: PDB / ID: 6ofx | |||||||||
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Title | Non-rotated ribosome (Structure I) | |||||||||
Components |
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Keywords | RIBOSOME / Ribosome recycling / translation termination / RF2 / intersubunit rotation | |||||||||
Function / homology | Function and homology information ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation ...ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / DnaA-L2 complex / four-way junction DNA binding / 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 / assembly of large subunit precursor of preribosome / positive regulation of RNA splicing / cytosolic ribosome assembly / transcription elongation factor complex / regulation of DNA-templated transcription elongation / DNA endonuclease activity / response to reactive oxygen species / transcription antitermination / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / 5S rRNA binding / transferase activity / small ribosomal subunit / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / molecular adaptor activity / 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 (E. coli) Escherichia coli K-12 (bacteria) synthetic construct (others) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Svidritskiy, E. / Demo, G. / Loveland, A.B. / Xu, C. / Korostelev, A.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Elife / Year: 2019 Title: Extensive ribosome and RF2 rearrangements during translation termination. Authors: Egor Svidritskiy / Gabriel Demo / Anna B Loveland / Chen Xu / Andrei A Korostelev / Abstract: Protein synthesis ends when a ribosome reaches an mRNA stop codon. Release factors (RFs) decode the stop codon, hydrolyze peptidyl-tRNA to release the nascent protein, and then dissociate to allow ...Protein synthesis ends when a ribosome reaches an mRNA stop codon. Release factors (RFs) decode the stop codon, hydrolyze peptidyl-tRNA to release the nascent protein, and then dissociate to allow ribosome recycling. To visualize termination by RF2, we resolved a cryo-EM ensemble of 70S•RF2 structures at up to 3.3 Å in a single sample. Five structures suggest a highly dynamic termination pathway. Upon peptidyl-tRNA hydrolysis, the CCA end of deacyl-tRNA departs from the peptidyl transferase center. The catalytic GGQ loop of RF2 is rearranged into a long β-hairpin that plugs the peptide tunnel, biasing a nascent protein toward the ribosome exit. Ribosomal intersubunit rotation destabilizes the catalytic RF2 domain on the 50S subunit and disassembles the central intersubunit bridge B2a, resulting in RF2 departure. Our structures visualize how local rearrangements and spontaneous inter-subunit rotation poise the newly-made protein and RF2 to dissociate in preparation for ribosome recycling. | |||||||||
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 | 6ofx.cif.gz | 3.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6ofx.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6ofx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ofx_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6ofx_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6ofx_validation.xml.gz | 182.1 KB | Display | |
Data in CIF | 6ofx_validation.cif.gz | 340.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/6ofx ftp://data.pdbj.org/pub/pdb/validation_reports/of/6ofx | HTTPS FTP |
-Related structure data
Related structure data | 20048MC 6og7C 6ogfC 6oggC 6ogiC 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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NMR ensembles |
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-Components
+50S ribosomal protein ... , 29 types, 29 molecules bcdefgjklmnopqrstuvwxyzBCDEFa
-30S ribosomal protein ... , 20 types, 20 molecules GHIJKLMNOPQRSTUVWXYZ
#29: Protein | Mass: 25015.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (strain K12) (bacteria) / Variant: MRE600 / Strain: K12 / References: UniProt: P0A7V0 |
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#30: Protein | Mass: 23078.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (strain K12) (bacteria) / Variant: MRE600 / Strain: K12 / References: UniProt: P0A7V3 |
#31: Protein | Mass: 23383.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (strain K12) (bacteria) / Variant: MRE600 / Strain: K12 / References: UniProt: P0A7V8 |
#32: Protein | Mass: 16532.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (strain K12) (bacteria) / Variant: MRE600 / Strain: K12 / References: UniProt: P0A7W1 |
#33: Protein | Mass: 11766.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (strain K12) (bacteria) / Variant: MRE600 / Strain: K12 / References: UniProt: P02358 |
#34: Protein | Mass: 16861.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (strain K12) (bacteria) / Variant: MRE600 / Strain: K12 / References: UniProt: P02359 |
#35: Protein | Mass: 14015.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (strain K12) (bacteria) / Variant: MRE600 / Strain: K12 / References: UniProt: P0A7W7 |
#36: Protein | Mass: 14554.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (strain K12) (bacteria) / Variant: MRE600 / Strain: K12 / References: UniProt: P0A7X3 |
#37: Protein | Mass: 11196.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (strain K12) (bacteria) / Variant: MRE600 / Strain: K12 / References: UniProt: P0A7R5 |
#38: Protein | Mass: 12388.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (strain K12) (bacteria) / Variant: MRE600 / Strain: K12 / References: UniProt: P0A7R9 |
#39: Protein | Mass: 13636.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (strain K12) (bacteria) / Variant: MRE600 / Strain: K12 / References: UniProt: P0A7S3 |
#40: Protein | Mass: 12625.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (strain K12) (bacteria) / Variant: MRE600 / Strain: K12 / References: UniProt: P0A7S9 |
#41: Protein | Mass: 11475.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (strain K12) (bacteria) / Variant: MRE600 / Strain: K12 / References: UniProt: P0AG59 |
#42: Protein | Mass: 10159.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (strain K12) (bacteria) / Variant: MRE600 / Strain: K12 / References: UniProt: P0ADZ4 |
#43: Protein | Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (strain K12) (bacteria) / Variant: MRE600 / Strain: K12 / References: UniProt: P0A7T3 |
#44: Protein | Mass: 9263.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (strain K12) (bacteria) / Variant: MRE600 / Strain: K12 / References: UniProt: P0AG63 |
#45: Protein | Mass: 7606.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (strain K12) (bacteria) / Variant: MRE600 / Strain: K12 / References: UniProt: P0A7T7 |
#46: Protein | Mass: 9057.626 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (strain K12) (bacteria) / Variant: MRE600 / Strain: K12 / References: UniProt: P0A7U3 |
#47: Protein | Mass: 9506.190 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (strain K12) (bacteria) / Variant: MRE600 / Strain: K12 / References: UniProt: P0A7U7 |
#48: Protein | Mass: 7763.073 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (strain K12) (bacteria) / Variant: MRE600 / Strain: K12 / References: UniProt: P68679 |
-RNA chain , 5 types, 5 molecules 31254
#50: RNA chain | Mass: 498725.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Variant: MRE600 / References: GenBank: 1126835768 |
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#51: RNA chain | Mass: 941305.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli K-12 (bacteria) / Variant: MRE600 / References: GenBank: 802133627 |
#52: RNA chain | Mass: 38813.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Variant: MRE600 / References: GenBank: 1266961702 |
#53: RNA chain | Mass: 24802.785 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) / References: GenBank: 1384458579 |
#54: RNA chain | Mass: 8878.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 1 types, 1 molecules
#55: Chemical | ChemComp-FME / |
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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: tRNAfMet bound to a non-rotated E. coli ribosome / Type: RIBOSOME / Entity ID: #1-#54 / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 2.5 MDa / Experimental value: NO |
Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
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 |
Image recording | Electron dose: 29.4 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: NONE |
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Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 102723 / Symmetry type: POINT |
NMR ensemble | Conformers submitted total number: 1 |