+Open data
-Basic information
Entry | Database: PDB / ID: 7old | ||||||
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Title | Thermophilic eukaryotic 80S ribosome at pe/E (TI)-POST state | ||||||
Components |
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Keywords | RIBOSOME / thermophilic eukaryotic ribosome / 80S / rRNA modifications / nascent chain | ||||||
Function / homology | Function and homology information RNA polymerase I core factor complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / RNA polymerase transcription factor SL1 complex / protein N-linked glycosylation via asparagine / RNA polymerase I core promoter sequence-specific DNA binding / protein kinase regulator activity / nucleolar large rRNA transcription by RNA polymerase I / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly ...RNA polymerase I core factor complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / RNA polymerase transcription factor SL1 complex / protein N-linked glycosylation via asparagine / RNA polymerase I core promoter sequence-specific DNA binding / protein kinase regulator activity / nucleolar large rRNA transcription by RNA polymerase I / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / translation elongation factor activity / translation regulator activity / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / cellular response to amino acid starvation / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / post-translational protein modification / maturation of LSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / positive regulation of apoptotic signaling pathway / methyltransferase activity / maturation of SSU-rRNA / small-subunit processome / protein kinase C binding / rRNA processing / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / methylation / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / GTPase activity / mRNA binding / nucleolus / GTP binding / RNA binding / zinc ion binding / membrane / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
Authors | Kisonaite, M. / Wild, K. / Sinning, I. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: High-resolution structures of a thermophilic eukaryotic 80S ribosome reveal atomistic details of translocation. Authors: Miglė Kišonaitė / Klemens Wild / Karine Lapouge / Thomas Ruppert / Irmgard Sinning / Abstract: Ribosomes are complex and highly conserved ribonucleoprotein assemblies catalyzing protein biosynthesis in every organism. Here we present high-resolution cryo-EM structures of the 80S ribosome from ...Ribosomes are complex and highly conserved ribonucleoprotein assemblies catalyzing protein biosynthesis in every organism. Here we present high-resolution cryo-EM structures of the 80S ribosome from a thermophilic fungus in two rotational states, which due to increased 80S stability provide a number of mechanistic details of eukaryotic translation. We identify a universally conserved 'nested base-triple knot' in the 26S rRNA at the polypeptide tunnel exit with a bulged-out nucleotide that likely serves as an adaptable element for nascent chain containment and handover. We visualize the structure and dynamics of the ribosome protective factor Stm1 upon ribosomal 40S head swiveling. We describe the structural impact of a unique and essential macp Ψ 18S rRNA hyper-modification embracing the anticodon wobble-position for eukaryotic tRNA and mRNA translocation. We complete the eEF2-GTPase switch cycle describing the GDP-bound post-hydrolysis state. Taken together, our data and their integration into the structural landscape of 80S ribosomes furthers our understanding of protein biogenesis. | ||||||
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 | 7old.cif.gz | 4.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7old.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7old.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ol/7old ftp://data.pdbj.org/pub/pdb/validation_reports/ol/7old | HTTPS FTP |
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-Related structure data
Related structure data | 12977MC 7olcC C: citing same article (ref.) M: map data used to model this data |
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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: 1078716.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) |
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#2: RNA chain | Mass: 578887.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) |
#3: RNA chain | Mass: 38596.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) |
#4: RNA chain | Mass: 50147.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) |
#5: RNA chain | Mass: 24004.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) |
-Protein , 6 types, 6 molecules ABCLhLmLs
#6: Protein | Mass: 35149.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S9U0 |
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#7: Protein | Mass: 32667.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S428 |
#8: Protein | Mass: 93786.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S5T7 |
#42: Protein | Mass: 14643.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 References: UniProt: G0S0D7, dolichyl-diphosphooligosaccharide-protein glycotransferase |
#47: Protein | Mass: 14481.093 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S8G4 |
#52: Protein | Mass: 33853.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SGP3 |
+60S ribosomal protein ... , 32 types, 33 molecules LALBLCLDLELFLGLHLILKLLLMLOLPLSLTLULVLWLXLYLZLaLbLcLeLfLiLkLn...
-Putative ribosomal ... , 2 types, 2 molecules LJSS
#18: Protein | Mass: 20119.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SHQ2 |
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#71: Protein | Mass: 17826.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S6J7 |
-Ribosomal protein ... , 8 types, 8 molecules LNLQLRLgLjLlSbSd
#22: Protein | Mass: 24307.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RZ88 |
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#25: Protein | Mass: 24195.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S9B5 |
#26: Protein | Mass: 22409.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S9T3 |
#41: Protein | Mass: 13492.993 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SFN0 |
#44: Protein | Mass: 10660.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S101 |
#46: Protein | Mass: 6297.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) References: UniProt: Q2H9R2 |
#80: Protein | Mass: 8923.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S1S4 |
#82: Protein | Mass: 6504.587 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) References: UniProt: Q2HB68 |
-Putative 60S ribosomal ... , 2 types, 2 molecules LdLq
#38: Protein | Mass: 13872.177 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SD68 |
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#51: Protein | Mass: 15960.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SHJ6 |
+40S ribosomal protein ... , 29 types, 29 molecules SASBSCSDSESFSGSHSISJSKSLSMSNSOSPSQSRSTSUSVSWSXSYSZSaScSeSf
-Non-polymers , 3 types, 12 molecules
#85: Chemical | #86: Chemical | ChemComp-GDP / | #87: Chemical | ChemComp-ZN / |
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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 |
-Sample preparation
Component | Name: Chaetomium thermophilum 80S ribosome / Type: CELL / Entity ID: #1-#84 / Source: NATURAL |
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Source (natural) | Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) |
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: 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 |
Image recording | Electron dose: 32.51 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35338 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 4V88 | ||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 146.57 Å2 | ||||||||||||||||||||||||||||
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