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Yorodumi- PDB-7k55: Near post-translocated +1-frameshifting(CCC-A) complex with EF-G ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7k55 | ||||||||||||
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Title | Near post-translocated +1-frameshifting(CCC-A) complex with EF-G and GDPCP (Structure III-FS) | ||||||||||||
Components |
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Keywords | RIBOSOME / EF-G / tRNA / TRANSLATION | ||||||||||||
Function / homology | Function and homology information negative regulation of cytoplasmic translational initiation / guanosine tetraphosphate binding / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity ...negative regulation of cytoplasmic translational initiation / guanosine tetraphosphate binding / stringent response / 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 / translation elongation factor activity / four-way junction DNA binding / translational termination / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / negative regulation of translational 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 / response to reactive oxygen species / transcription antitermination / 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 / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit assembly / ribosomal large subunit assembly / small ribosomal subunit / transferase activity / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic small ribosomal subunit / 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 / GTPase activity / mRNA binding / GTP binding / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Escherichia coli K-12 (bacteria) Escherichia coli (E. coli) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||
Authors | Demo, G. / Loveland, A.B. / Svidritskiy, E. / Gamper, H.B. / Hou, Y.M. / Korostelev, A.A. | ||||||||||||
Funding support | United States, Czech Republic, 3items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structural basis for +1 ribosomal frameshifting during EF-G-catalyzed translocation. Authors: Gabriel Demo / Howard B Gamper / Anna B Loveland / Isao Masuda / Christine E Carbone / Egor Svidritskiy / Ya-Ming Hou / Andrei A Korostelev / Abstract: Frameshifting of mRNA during translation provides a strategy to expand the coding repertoire of cells and viruses. How and where in the elongation cycle +1-frameshifting occurs remains poorly ...Frameshifting of mRNA during translation provides a strategy to expand the coding repertoire of cells and viruses. How and where in the elongation cycle +1-frameshifting occurs remains poorly understood. We describe seven ~3.5-Å-resolution cryo-EM structures of 70S ribosome complexes, allowing visualization of elongation and translocation by the GTPase elongation factor G (EF-G). Four structures with a + 1-frameshifting-prone mRNA reveal that frameshifting takes place during translocation of tRNA and mRNA. Prior to EF-G binding, the pre-translocation complex features an in-frame tRNA-mRNA pairing in the A site. In the partially translocated structure with EF-G•GDPCP, the tRNA shifts to the +1-frame near the P site, rendering the freed mRNA base to bulge between the P and E sites and to stack on the 16S rRNA nucleotide G926. The ribosome remains frameshifted in the nearly post-translocation state. Our findings demonstrate that the ribosome and EF-G cooperate to induce +1 frameshifting during tRNA-mRNA translocation. | ||||||||||||
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 | 7k55.cif.gz | 3.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7k55.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7k55.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7k55_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7k55_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7k55_validation.xml.gz | 216.2 KB | Display | |
Data in CIF | 7k55_validation.cif.gz | 386.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/7k55 ftp://data.pdbj.org/pub/pdb/validation_reports/k5/7k55 | HTTPS FTP |
-Related structure data
Related structure data | 22674MC 7k50C 7k51C 7k52C 7k53C 7k54C 7lv0C 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
+50S ribosomal protein ... , 32 types, 32 molecules bcdefghijklmnopqrstuvwxyzABCDEFa
-30S ribosomal protein ... , 20 types, 20 molecules GHIJKLMNOPQRSTUVWXYZ
#32: 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) / Strain: K12 / References: UniProt: P0A7V0 |
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#33: 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) / Strain: K12 / References: UniProt: P0A7V3 |
#34: 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) / Strain: K12 / References: UniProt: P0A7V8 |
#35: 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) / Strain: K12 / References: UniProt: P0A7W1 |
#36: Protein | Mass: 11669.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: UniProt: P02358 |
#37: 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) / Strain: K12 / References: UniProt: P02359 |
#38: 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) / Strain: K12 / References: UniProt: P0A7W7 |
#39: 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) / Strain: K12 / References: UniProt: P0A7X3 |
#40: 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) / Strain: K12 / References: UniProt: P0A7R5 |
#41: 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) / Strain: K12 / References: UniProt: P0A7R9 |
#42: 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) / Strain: K12 / References: UniProt: P0A7S3 |
#43: 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) / Strain: K12 / References: UniProt: P0A7S9 |
#44: 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) / Strain: K12 / References: UniProt: P0AG59 |
#45: 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) / Strain: K12 / References: UniProt: P0ADZ4 |
#46: 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) / Strain: K12 / References: UniProt: P0A7T3 |
#47: 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) / Strain: K12 / References: UniProt: P0AG63 |
#48: 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) / Strain: K12 / References: UniProt: P0A7T7 |
#49: 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) / Strain: K12 / References: UniProt: P0A7U3 |
#50: 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) / Strain: K12 / References: UniProt: P0A7U7 |
#51: 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) / Strain: K12 / References: UniProt: P68679 |
-RNA chain , 6 types, 6 molecules 312564
#53: RNA chain | Mass: 498725.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: GenBank: 1126835768 |
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#54: RNA chain | Mass: 941305.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: GenBank: 802133627 |
#55: RNA chain | Mass: 38813.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: GenBank: 1266961702 |
#56: RNA chain | Mass: 24862.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: GenBank: 1848949880 |
#57: RNA chain | Mass: 24802.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12 / References: GenBank: 1275521620 |
#58: RNA chain | Mass: 5168.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli K-12 (bacteria) |
-Protein , 1 types, 1 molecules 8
#59: Protein | Mass: 78616.203 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: fusA, HMPREF1591_03890 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: U9XYS4 |
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-Non-polymers , 4 types, 4 molecules
#60: Chemical | ChemComp-FME / |
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#61: Chemical | ChemComp-PRO / |
#62: Chemical | ChemComp-GCP / |
#63: Chemical | ChemComp-MG / |
-Details
Has ligand of interest | 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: Near post-translocated +1-frameshifting(CCC-A) ribosome complex Type: RIBOSOME / Entity ID: #1-#59 / Source: NATURAL | |||||||||||||||||||||||||||||||||||
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Molecular weight | Value: 1.6 MDa / Experimental value: NO | |||||||||||||||||||||||||||||||||||
Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) / Strain: MRE600 | |||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||||||||||||
Specimen support | Details: glow discharged with 25mA negative polarity in PELCO easiGlow unit Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 | |||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 278 K / Details: blotting force 9, blotted for 4 seconds |
-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 / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 47.5 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 2591 |
Image scans | Movie frames/image: 36 / Used frames/image: 1-36 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 164504 | |||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6029 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: correlation coefficient | |||||||||||||||||||||||||||||||||||
Atomic model building |
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