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Yorodumi- PDB-6gz3: tRNA translocation by the eukaryotic 80S ribosome and the impact ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gz3 | ||||||||||||
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Title | tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-1 (TI-POST-1) | ||||||||||||
Components |
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Keywords | RIBOSOME / translocation rabbit ribosome / 80S / eEF2 / head swivel / rotation | ||||||||||||
Function / homology | Function and homology information Ribosomal protein S12e signature. / Ribosomal protein S27a / 40S Ribosomal protein S10 / Plectin/S10, N-terminal / Ribosomal protein L44 / Plectin/S10 domain / Ribosomal L27e protein family / Ribosomal protein L1 signature. / Ribosomal protein S17e signature. / Ribosomal protein S28e ...Ribosomal protein S12e signature. / Ribosomal protein S27a / 40S Ribosomal protein S10 / Plectin/S10, N-terminal / Ribosomal protein L44 / Plectin/S10 domain / Ribosomal L27e protein family / Ribosomal protein L1 signature. / Ribosomal protein S17e signature. / Ribosomal protein S28e / Ribosomal protein L44e signature. / Ribosomal protein L27e signature. / Ribosomal protein L10e signature. / Ribosomal protein S7e signature. / Ribosomal protein S6e / Ribosomal L37ae protein family / Ribosomal protein S3Ae signature. / Ribosomal protein L24e signature. / Ribosomal protein L39e signature. / Ribosomal protein L31e / Ribosomal protein S6e signature. / Ribosomal L39 protein / Ribosomal protein S28e signature. / Ribosomal protein L37e / Ribosomal L15 / Ribosomal protein L32 / Ribosomal protein L31e signature. / Ribosomal protein L1p/L10e family / Ribosomal proteins L26 eukaryotic, L24P archaeal / Ribosomal protein L32e signature. / Ribosomal protein L15e signature. / Ribosomal protein L21e signature. / Ribosomal protein L37e signature. / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11, RNA binding domain / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein S14 signature. / Ribosomal protein L5 signature. / Ribosomal protein L5 / Ribosomal protein S4/S9 N-terminal domain / ribosomal L5P family C-terminus / Ribosomal protein S13/S18 / Ribosomal protein L16p/L10e / Ribosomal protein S14p/S29e / Ribosomal protein S7 signature. / Ribosomal protein S8 / Ribosomal protein S17 signature. / Ribosomal protein S13 signature. / Ribosomal protein S13 family profile. / Ribosomal protein S8 signature. / S4 domain / Ribosomal protein S4 signature. / Ribosomal protein S15 signature. / Ribosomal protein S7p/S5e / S4 RNA-binding domain profile. / Ribosomal protein S12/S23 / Ribosomal protein S17 / Ribosomal protein S15 / Ribosomal protein L14 signature. / Ubiquitin domain profile. / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S12 signature. / Ribosomal protein L24 signature. / Ribosomal protein L14p/L23e / KOW motif / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / Winged helix-like DNA-binding domain superfamily Similarity search - Domain/homology | ||||||||||||
Biological species | Enterobacteria phage SP6 (virus) Oryctolagus cuniculus (rabbit) Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||
Authors | Flis, J. / Holm, M. / Rundlet, E.J. / Loerke, J. / Hilal, T. / Dabrowski, M. / Buerger, J. / Mielke, T. / Blanchard, S.C. / Spahn, C.M.T. / Budkevich, T.V. | ||||||||||||
Funding support | Germany, United States, 3items
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Citation | Journal: Cell Rep / Year: 2018 Title: tRNA Translocation by the Eukaryotic 80S Ribosome and the Impact of GTP Hydrolysis. Authors: Julia Flis / Mikael Holm / Emily J Rundlet / Justus Loerke / Tarek Hilal / Marylena Dabrowski / Jörg Bürger / Thorsten Mielke / Scott C Blanchard / Christian M T Spahn / Tatyana V Budkevich / Abstract: Translocation moves the tRNA⋅mRNA module directionally through the ribosome during the elongation phase of protein synthesis. Although translocation is known to entail large conformational changes ...Translocation moves the tRNA⋅mRNA module directionally through the ribosome during the elongation phase of protein synthesis. Although translocation is known to entail large conformational changes within both the ribosome and tRNA substrates, the orchestrated events that ensure the speed and fidelity of this critical aspect of the protein synthesis mechanism have not been fully elucidated. Here, we present three high-resolution structures of intermediates of translocation on the mammalian ribosome where, in contrast to bacteria, ribosomal complexes containing the translocase eEF2 and the complete tRNA⋅mRNA module are trapped by the non-hydrolyzable GTP analog GMPPNP. Consistent with the observed structures, single-molecule imaging revealed that GTP hydrolysis principally facilitates rate-limiting, final steps of translocation, which are required for factor dissociation and which are differentially regulated in bacterial and mammalian systems by the rates of deacyl-tRNA dissociation from the E site. | ||||||||||||
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 | 6gz3.cif.gz | 4.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6gz3.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6gz3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/6gz3 ftp://data.pdbj.org/pub/pdb/validation_reports/gz/6gz3 | HTTPS FTP |
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-Related structure data
Related structure data | 0098MC 0099C 0100C 6gz4C 6gz5C 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 , 7 types, 7 molecules A2BvBxBwB1A3A4
#1: RNA chain | Mass: 1170164.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
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#2: RNA chain | Mass: 24437.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
#3: RNA chain | Mass: 3837.328 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage SP6 (virus) / Production host: Enterobacteria phage SP6 (virus) |
#4: RNA chain | Mass: 24533.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 176421 |
#5: RNA chain | Mass: 551108.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
#39: RNA chain | Mass: 50449.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
#40: RNA chain | Mass: 38385.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
+Ribosomal protein ... , 72 types, 72 molecules BDBFBKBPBQBRBSBTBUBZBcBdBfBgBABCBEBIBJBLBNBOBVBWBXBYBaBbBeAA...
-40S ribosomal protein ... , 4 types, 4 molecules BMBBBGBH
#9: Protein | Mass: 13393.658 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SFR8 |
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#22: Protein | Mass: 24660.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SS70 |
#25: Protein | Mass: 26913.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM55 |
#26: Protein | Mass: 20990.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVB0 |
-Protein , 3 types, 3 molecules AZAuCt
#65: Protein | Mass: 15647.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TXF6 |
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#83: Protein | Mass: 24879.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKZ8 |
#86: Protein | Mass: 95056.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
-Non-polymers , 3 types, 333 molecules
#87: Chemical | ChemComp-MG / #88: Chemical | ChemComp-ZN / #89: Chemical | ChemComp-GNP / | |
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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 |
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Molecular weight | Value: 4.3 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Enterobacteria phage SP6 (virus) | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-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 FIELDBright-field microscopy |
Image recording | Average exposure time: 5 sec. / Electron dose: 30 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Particle selection | Num. of particles selected: 270000 |
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32386 / Symmetry type: POINT |
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL |