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Open data
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Basic information
Entry | Database: PDB / ID: 7olc | ||||||
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Title | Thermophilic eukaryotic 80S ribosome at idle POST state | ||||||
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![]() | RIBOSOME / thermophilic eukaryotic ribosome / 80S / rRNA modifications / nascent chain | ||||||
Function / homology | ![]() RNA polymerase I core factor complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine / RNA polymerase transcription factor SL1 complex / RNA polymerase I core promoter sequence-specific DNA binding / protein kinase regulator activity / non-chaperonin molecular chaperone ATPase / 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) ...RNA polymerase I core factor complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine / RNA polymerase transcription factor SL1 complex / RNA polymerase I core promoter sequence-specific DNA binding / protein kinase regulator activity / non-chaperonin molecular chaperone ATPase / 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 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) / 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) / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / post-translational protein modification / maturation of LSU-rRNA / ribosomal large subunit biogenesis / methyltransferase activity / maturation of SSU-rRNA / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / ATP-dependent protein folding chaperone / 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 / mRNA binding / nucleolus / ATP hydrolysis activity / RNA binding / zinc ion binding / ATP binding / membrane / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||
![]() | Kisonaite, M. / Wild, K. / Sinning, I. | ||||||
Funding support | ![]()
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![]() | ![]() 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
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 4.6 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 279.1 KB | Display | |
Data in CIF | ![]() | 480.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 12976MC ![]() 7oldC 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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Components
-RNA chain , 4 types, 4 molecules 1234
#1: RNA chain | Mass: 1078730.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() |
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#2: RNA chain | Mass: 578887.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() |
#3: RNA chain | Mass: 38596.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() |
#4: RNA chain | Mass: 50147.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() |
-Protein , 8 types, 8 molecules ABCLhLlLmLsSd
#5: Protein | Mass: 35149.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: G0S9U0 |
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#6: Protein | Mass: 32667.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: G0S428 |
#7: Protein | Mass: 67110.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: G0SCU5, non-chaperonin molecular chaperone ATPase |
#41: Protein | Mass: 14643.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: G0S0D7, dolichyl-diphosphooligosaccharide-protein glycotransferase |
#45: Protein | Mass: 6297.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q2H9R2 |
#46: Protein | Mass: 14609.222 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: G0S8G4 |
#51: Protein | Mass: 33853.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: G0SGP3 |
#81: Protein | Mass: 6504.587 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q2HB68 |
+60S ribosomal protein ... , 32 types, 33 molecules LALBLCLDLELFLGLHLILKLLLMLOLPLSLTLULVLWLXLYLZLaLbLcLeLfLiLkLn...
-Putative ribosomal ... , 2 types, 2 molecules LJSS
#17: Protein | Mass: 20119.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: G0SHQ2 |
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#70: Protein | Mass: 17826.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: G0S6J7 |
-Ribosomal protein ... , 6 types, 6 molecules LNLQLRLgLjSb
#21: Protein | Mass: 24307.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: G0RZ88 |
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#24: Protein | Mass: 24195.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: G0S9B5 |
#25: Protein | Mass: 22409.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: G0S9T3 |
#40: Protein | Mass: 13492.993 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: G0SFN0 |
#43: Protein | Mass: 10660.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: G0S101 |
#79: Protein | Mass: 8923.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: G0S1S4 |
-Putative 60S ribosomal ... , 2 types, 2 molecules LdLq
#37: Protein | Mass: 13872.177 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: G0SD68 |
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#50: Protein | Mass: 15960.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: G0SHJ6 |
+40S ribosomal protein ... , 29 types, 29 molecules SASBSCSDSESFSGSHSISJSKSLSMSNSOSPSQSRSTSUSVSWSXSYSZSaScSeSf
-Non-polymers , 3 types, 1524 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#84: Chemical | ChemComp-MG / #85: Chemical | ChemComp-ZN / #86: Water | ChemComp-HOH / | |
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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: Chaetomium thermophilum 80S ribosome / Type: CELL / Entity ID: #1-#83 / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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 |
Image recording | Electron dose: 32.51 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
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Processing
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 279818 / 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: 136.02 Å2 | ||||||||||||||||||||||||||||
Refine LS restraints |
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