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- PDB-7k55: Near post-translocated +1-frameshifting(CCC-A) complex with EF-G ... -
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Open data
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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) | ||||||||||||
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Function / homology | ![]() negative regulation of cytoplasmic translational initiation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | 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
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 3.3 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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 ( |
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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, 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) ![]() ![]() ![]() |
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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: 24862.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() ![]() |
#57: RNA chain | Mass: 24802.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() ![]() |
#58: RNA chain | ![]() Mass: 5168.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() ![]() |
-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.) ![]() ![]() ![]() Production host: ![]() ![]() ![]() References: UniProt: U9XYS4 |
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-Non-polymers , 4 types, 4 molecules ![](data/chem/img/FME.gif)
![](data/chem/img/PRO.gif)
![](data/chem/img/GCP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PRO.gif)
![](data/chem/img/GCP.gif)
![](data/chem/img/MG.gif)
#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: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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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: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | |||||||||||||||||||||||||||||||||||
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 |
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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![]() |
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 |
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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: 164504 | |||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry![]() | |||||||||||||||||||||||||||||||||||
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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