+Open data
-Basic information
Entry | Database: PDB / ID: 6ouo | ||||||||||||
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Title | RF2 accommodated state bound 70S complex at long incubation time | ||||||||||||
Components |
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Keywords | RIBOSOME / Time-resolved cryo-EM / Termination / short-lived / millisecond | ||||||||||||
Function / homology | Function and homology information translation release factor activity, codon specific / 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 / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity ...translation release factor activity, codon specific / 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 / 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 / translational termination / 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 / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / DNA endonuclease activity / ribosomal large subunit assembly / 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 / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / molecular adaptor activity / 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 / membrane / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||
Authors | Fu, Z. / Indrisiunaite, G. / Kaledhonkar, S. / Shah, B. / Sun, M. / Chen, B. / Grassucci, R.A. / Ehrenberg, M. / Frank, J. | ||||||||||||
Funding support | United States, Sweden, 3items
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Citation | Journal: Nat Commun / Year: 2019 Title: The structural basis for release-factor activation during translation termination revealed by time-resolved cryogenic electron microscopy. Authors: Ziao Fu / Gabriele Indrisiunaite / Sandip Kaledhonkar / Binita Shah / Ming Sun / Bo Chen / Robert A Grassucci / Måns Ehrenberg / Joachim Frank / Abstract: When the ribosome encounters a stop codon, it recruits a release factor (RF) to hydrolyze the ester bond between the peptide chain and tRNA. RFs have structural motifs that recognize stop codons in ...When the ribosome encounters a stop codon, it recruits a release factor (RF) to hydrolyze the ester bond between the peptide chain and tRNA. RFs have structural motifs that recognize stop codons in the decoding center and a GGQ motif for induction of hydrolysis in the peptidyl transfer center 70 Å away. Surprisingly, free RF2 is compact, with only 20 Å between its codon-reading and GGQ motifs. Cryo-EM showed that ribosome-bound RFs have extended structures, suggesting that RFs are compact when entering the ribosome and then extend their structures upon stop codon recognition. Here we use time-resolved cryo-EM to visualize transient compact forms of RF1 and RF2 at 3.5 and 4 Å resolution, respectively, in the codon-recognizing ribosome complex on the native pathway. About 25% of complexes have RFs in the compact state at 24 ms reaction time, and within 60 ms virtually all ribosome-bound RFs are transformed to their extended forms. | ||||||||||||
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 | 6ouo.cif.gz | 3.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6ouo.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6ouo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ouo_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6ouo_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6ouo_validation.xml.gz | 198.8 KB | Display | |
Data in CIF | 6ouo_validation.cif.gz | 354.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/6ouo ftp://data.pdbj.org/pub/pdb/validation_reports/ou/6ouo | HTTPS FTP |
-Related structure data
Related structure data | 20204MC 6oreC 6orlC 6oskC 6osqC 6ostC 6ot3C 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 12345
#1: RNA chain | Mass: 941526.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
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#2: RNA chain | Mass: 497404.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
#3: 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: 1273279017 |
#4: RNA chain | Mass: 2754.647 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
#54: RNA chain | Mass: 24565.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
+50S ribosomal protein ... , 29 types, 29 molecules BCDEFGJKLMNOPQRSTUVWXYZabcdef
-30S ribosomal protein ... , 20 types, 20 molecules ghijklmnopqrstuvwxyz
#34: Protein | Mass: 25072.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C3TPN2, UniProt: P0A7V0*PLUS |
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#35: Protein | Mass: 23248.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A376HTV6, UniProt: P0A7V3*PLUS |
#36: Protein | Mass: 23383.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: L3PZ69, UniProt: P0A7V8*PLUS |
#37: Protein | Mass: 16475.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: A0A073FR78, UniProt: P0A7W1*PLUS |
#38: Protein | Mass: 12125.993 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A376ZL25, UniProt: P02358*PLUS |
#39: Protein | Mass: 16861.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: S1D5F0, UniProt: P02359*PLUS |
#40: Protein | Mass: 14015.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D8A1L7, UniProt: P0A7W7*PLUS |
#41: Protein | Mass: 14554.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: T9TH92, UniProt: P0A7X3*PLUS |
#42: Protein | Mass: 11254.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: J7RLQ6, UniProt: P0A7R5*PLUS |
#43: Protein | Mass: 12487.200 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7R9 |
#44: Protein | Mass: 9630.292 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A377DM03, UniProt: P0A7S3*PLUS |
#45: Protein | Mass: 12868.091 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: A0A1X3JB38, UniProt: P0A7S9*PLUS |
#46: Protein | Mass: 11475.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: J7R6H7, UniProt: P0AG59*PLUS |
#47: Protein | Mass: 10159.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7XN21, UniProt: P0ADZ4*PLUS |
#48: Protein | Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MIU7, UniProt: P0A7T3*PLUS |
#49: Protein | Mass: 9263.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A080IK26, UniProt: P0AG63*PLUS |
#50: Protein | Mass: 7734.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7ZI16, UniProt: P0A7T7*PLUS |
#51: Protein | Mass: 9421.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: A0A0A8UF41, UniProt: P0A7U3*PLUS |
#52: Protein | Mass: 9577.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: I4T5W9, UniProt: P0A7U7*PLUS |
#53: Protein | Mass: 8392.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli / References: UniProt: L3C5D9, UniProt: P68679*PLUS |
-Protein , 1 types, 1 molecules A
#55: Protein | Mass: 40424.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A2S5ZJX2, UniProt: P07012*PLUS |
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-Non-polymers , 2 types, 14 molecules
#56: Chemical | ChemComp-MG / #57: Chemical | |
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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: Release complex 70S ribosomes / Type: RIBOSOME / Entity ID: #1-#55 / Source: NATURAL |
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Molecular weight | Units: MEGADALTONS / Experimental value: NO |
Source (natural) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 41.6 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: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 94709 / Symmetry type: POINT |