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Yorodumi- PDB-6ogg: 70S termination complex with RF2 bound to the UGA codon. Rotated ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ogg | |||||||||
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Title | 70S termination complex with RF2 bound to the UGA codon. Rotated ribosome with RF2 bound (Structure IV). | |||||||||
Components |
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Keywords | RIBOSOME / Ribosome recycling / translation termination / RF2 / intersubunit rotation | |||||||||
Function / homology | Function and homology information translation release factor activity, codon specific / positive regulation of ribosome biogenesis / DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / regulation of cell growth / small ribosomal subunit rRNA binding / large ribosomal subunit / ribosome binding ...translation release factor activity, codon specific / positive regulation of ribosome biogenesis / DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / regulation of cell growth / small ribosomal subunit rRNA binding / large ribosomal subunit / ribosome binding / regulation of translation / small ribosomal subunit / 5S rRNA binding / transferase activity / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) synthetic construct (others) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 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 | 6ogg.cif.gz | 3.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6ogg.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6ogg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ogg_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6ogg_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6ogg_validation.xml.gz | 192.3 KB | Display | |
Data in CIF | 6ogg_validation.cif.gz | 346.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/6ogg ftp://data.pdbj.org/pub/pdb/validation_reports/og/6ogg | HTTPS FTP |
-Related structure data
Related structure data | 20057MC 6ofxC 6og7C 6ogfC 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: 26781.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7ZK99 |
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#30: Protein | Mass: 26031.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MCS9 |
#31: Protein | Mass: 23514.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7Z9H7 |
#32: Protein | Mass: 17629.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7Z9H2 |
#33: Protein | Mass: 15211.058 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7ZI17 |
#34: Protein | Mass: 17637.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7ZAN1 |
#35: Protein | Mass: 14146.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7Z9G9 |
#36: Protein | Mass: 14886.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7ZES9 |
#37: Protein | Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7Z9F4 |
#38: Protein | Mass: 13870.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: B7MCR3 |
#39: Protein | Mass: 13768.157 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7ZAN0 |
#40: Protein | Mass: 13128.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: H4UQ02 |
#41: Protein | Mass: 11606.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7Z9G8 |
#42: Protein | Mass: 10290.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7ZEL4 |
#43: Protein | Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MIU7 |
#44: Protein | Mass: 9724.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7Z9G4 |
#45: Protein | Mass: 9005.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: A0A0E2KXL3 |
#46: Protein | Mass: 10455.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7Z9F9 |
#47: Protein | Mass: 9708.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: D7ZAS2 |
#48: Protein | Mass: 8524.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (E. coli) / Strain: MRE600 / References: UniProt: A0A0E2L2J1 |
-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) / References: GenBank: 1338015391 |
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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 (E. coli) / References: GenBank: 1036415628 |
#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) / References: GenBank: 1370526515 |
#53: RNA chain | Mass: 24802.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) 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) |
-Protein , 1 types, 1 molecules 8
#55: Protein | Mass: 42129.535 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: prfB, C4J69_20115 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S5ZJX2 |
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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 and RF2 bound to a rotated E. coli ribosome / Type: RIBOSOME / Entity ID: all / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 2.5 MDa / Experimental value: NO |
Source (natural) | Organism: Escherichia coli (E. coli) / Strain: MRE600 |
Buffer solution | pH: 7 |
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 |
Image recording | Electron dose: 29.4 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5881 / Symmetry type: POINT |
NMR ensemble | Conformers submitted total number: 1 |