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Open data
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Basic information
Entry | Database: PDB / ID: 7k50 | ||||||||||||
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Title | Pre-translocation non-frameshifting(CCA-A) complex (Structure I) | ||||||||||||
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![]() | RIBOSOME / tRNA / TRANSLATION | ||||||||||||
Function / homology | ![]() negative regulation of cytoplasmic translational initiation / stringent response / mRNA base-pairing translational repressor activity / 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 / stringent response / mRNA base-pairing translational repressor activity / 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 / translational termination / 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 / translational initiation / ribosome assembly / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / DNA endonuclease activity / regulation of DNA-templated transcription elongation / cytosolic ribosome assembly / transcription antitermination / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / ribosomal large subunit assembly / 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 / tRNA binding / cytoplasmic translation / molecular adaptor activity / rRNA binding / negative regulation of translation / 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 / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||||||||
![]() | Demo, G. / Loveland, A.B. / Svidritskiy, E. / Gamper, H.B. / Hou, Y.M. / Korostelev, A.A. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 3.2 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 197 KB | Display | |
Data in CIF | ![]() | 355.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 22669MC ![]() 7k51C ![]() 7k52C ![]() 7k53C ![]() 7k54C ![]() 7k55C ![]() 7lv0C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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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) ![]() ![]() |
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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) ![]() ![]() |
#34: Protein | Mass: 23383.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#35: Protein | Mass: 16532.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#36: Protein | Mass: 11669.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#37: Protein | Mass: 16861.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#38: Protein | Mass: 14015.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#39: Protein | Mass: 14554.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#40: Protein | Mass: 11196.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#41: Protein | Mass: 12388.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#42: Protein | Mass: 13636.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#43: Protein | Mass: 12625.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#44: Protein | Mass: 11475.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#45: Protein | Mass: 10159.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#46: Protein | Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#47: Protein | Mass: 9263.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#48: Protein | Mass: 7606.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#49: Protein | Mass: 9057.626 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#50: Protein | Mass: 9506.190 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
#51: Protein | Mass: 7763.073 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
-RNA chain , 6 types, 7 molecules 3125647
#53: RNA chain | Mass: 498725.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() | ||||
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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) ![]() ![]() | ||||
#55: RNA chain | Mass: 38813.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() | ||||
#56: RNA chain | Mass: 24802.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() #57: RNA chain | | Mass: 5866.619 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #58: RNA chain | | Mass: 24862.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() |
-Non-polymers , 1 types, 1 molecules ![](data/chem/img/FME.gif)
#59: Chemical | ChemComp-FME / |
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-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 |
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Sample preparation
Component | Name: Pre-translocation non-frameshifting(CCA-A) ribosome complex Type: RIBOSOME / Entity ID: #1-#58 / Source: NATURAL | |||||||||||||||||||||||||||||||||||
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Molecular weight | Value: 1.6 MDa / Experimental value: NO | |||||||||||||||||||||||||||||||||||
Source (natural) | Organism: ![]() ![]() | |||||||||||||||||||||||||||||||||||
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 with 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 |
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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: ![]() |
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 | Average exposure time: 7.2 sec. / Electron dose: 47.5 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 1041 |
Image scans | Movie frames/image: 36 / Used frames/image: 1-36 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 62716 | |||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4263 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: correlation coefficient | |||||||||||||||||||||||||||||||||
Atomic model building |
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