+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12976 | |||||||||
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Title | Thermophilic eukaryotic 80S ribosome at idle POST state | |||||||||
Map data | ||||||||||
Sample |
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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 / 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 / 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 / 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) / 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 / 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 / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Kisonaite M / Wild K / Sinning I | |||||||||
Funding support | Germany, 1 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12976.map.gz | 174.7 MB | EMDB map data format | |
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Header (meta data) | emd-12976-v30.xml emd-12976.xml | 94.6 KB 94.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12976_fsc.xml | 18.7 KB | Display | FSC data file |
Images | emd_12976.png | 189.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12976 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12976 | HTTPS FTP |
-Related structure data
Related structure data | 7olcMC 7oldC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12976.map.gz / Format: CCP4 / Size: 437.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Chaetomium thermophilum 80S ribosome
+Supramolecule #1: Chaetomium thermophilum 80S ribosome
+Macromolecule #1: 26S rRNA
+Macromolecule #2: 18S rRNA
+Macromolecule #3: 5S rRNA
+Macromolecule #4: 5.8S rRNA
+Macromolecule #5: Putative guanine nucleotide-binding protein
+Macromolecule #6: HABP4_PAI-RBP1 domain-containing protein
+Macromolecule #7: Ribosome-associated molecular chaperone SSB1
+Macromolecule #8: 60S ribosomal protein L2-like protein
+Macromolecule #9: 60S ribosomal protein L3-like protein
+Macromolecule #10: 60S ribosomal protein L4-like protein
+Macromolecule #11: 60S ribosomal protein l5-like protein
+Macromolecule #12: 60S ribosomal protein L6
+Macromolecule #13: 60S ribosomal protein l7-like protein
+Macromolecule #14: 60S ribosomal protein L8
+Macromolecule #15: 60S ribosomal protein l9-like protein
+Macromolecule #16: 60S ribosomal protein L10-like protein
+Macromolecule #17: Putative ribosomal protein
+Macromolecule #18: 60S ribosomal protein L12-like protein
+Macromolecule #19: 60S ribosomal protein L13
+Macromolecule #20: 60S ribosomal protein L14-like protein
+Macromolecule #21: Ribosomal protein L15
+Macromolecule #22: 60S ribosomal protein L16-like protein
+Macromolecule #23: 60S ribosomal protein l17-like protein
+Macromolecule #24: Ribosomal protein L18-like protein
+Macromolecule #25: Ribosomal protein L19
+Macromolecule #26: 60S ribosomal protein L20
+Macromolecule #27: 60S ribosomal protein l21-like protein
+Macromolecule #28: 60S ribosomal protein L22-like protein
+Macromolecule #29: 60S ribosomal protein l23-like protein
+Macromolecule #30: 60S ribosomal protein L24-like protein
+Macromolecule #31: 60S ribosomal protein L25-like protein
+Macromolecule #32: 60S ribosomal protein L26-like protein
+Macromolecule #33: 60S ribosomal protein L27
+Macromolecule #34: 60S ribosomal protein L28-like protein
+Macromolecule #35: 60S ribosomal protein L29
+Macromolecule #36: 60S ribosomal protein l30-like protein
+Macromolecule #37: Putative 60S ribosomal protein
+Macromolecule #38: 60S ribosomal protein L32-like protein
+Macromolecule #39: 60S ribosomal protein l33-like protein
+Macromolecule #40: Ribosomal protein l34-like protein
+Macromolecule #41: Dolichyl-diphosphooligosaccharide--protein glycotransferase
+Macromolecule #42: 60S ribosomal protein L36
+Macromolecule #43: Ribosomal protein L37
+Macromolecule #44: 60S ribosomal protein L38-like protein
+Macromolecule #45: eL39
+Macromolecule #46: Ubiquitin
+Macromolecule #47: 60S ribosomal protein L41-A
+Macromolecule #48: 60S ribosomal protein L44-like protein
+Macromolecule #49: 60S ribosomal protein L43-like protein
+Macromolecule #50: Putative 60S ribosomal protein
+Macromolecule #51: 60S acidic ribosomal protein P0
+Macromolecule #52: 40S ribosomal protein S0
+Macromolecule #53: 40S ribosomal protein S1
+Macromolecule #54: 40S ribosomal protein S2-like protein
+Macromolecule #55: 40S ribosomal protein S3-like protein
+Macromolecule #56: 40S ribosomal protein S4
+Macromolecule #57: 40S ribosomal protein s5-like protein
+Macromolecule #58: 40S ribosomal protein S6
+Macromolecule #59: 40S ribosomal protein S7
+Macromolecule #60: 40S ribosomal protein S8
+Macromolecule #61: 40S ribosomal protein s9-like protein
+Macromolecule #62: 40S ribosomal protein s10-like protein
+Macromolecule #63: 40S ribosomal protein S11-like protein
+Macromolecule #64: 40S ribosomal protein S12
+Macromolecule #65: 40S ribosomal protein S13-like protein
+Macromolecule #66: 40S ribosomal protein S14-like protein
+Macromolecule #67: 40S ribosomal protein s15-like protein
+Macromolecule #68: 40S ribosomal protein S16-like protein
+Macromolecule #69: 40S ribosomal protein S17-like protein
+Macromolecule #70: Putative ribosomal protein
+Macromolecule #71: 40S ribosomal protein S19-like protein
+Macromolecule #72: 40S ribosomal protein S20-like protein
+Macromolecule #73: 40S ribosomal protein S21-like protein
+Macromolecule #74: 40S ribosomal protein S22-like protein
+Macromolecule #75: 40S ribosomal protein s23-like protein
+Macromolecule #76: 40S ribosomal protein S24
+Macromolecule #77: 40S ribosomal protein S25
+Macromolecule #78: 40S ribosomal protein S26
+Macromolecule #79: Ribosomal protein s27-like protein
+Macromolecule #80: 40S ribosomal protein S28-like protein
+Macromolecule #81: uS14
+Macromolecule #82: 40S ribosomal protein S30
+Macromolecule #83: 40S ribosomal protein S27a-like protein
+Macromolecule #84: MAGNESIUM ION
+Macromolecule #85: ZINC ION
+Macromolecule #86: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 32.51 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |