+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4214 | |||||||||
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Title | Structure of a eukaryotic cytoplasmic pre-40S ribosomal subunit | |||||||||
Map data | ||||||||||
Sample |
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Keywords | pre-40S ribosme / cryo-EM / ribosome assembly / ribosomes / ribosome biogenesis / RIBOSOME | |||||||||
Function / homology | Function and homology information positive regulation of RNA import into nucleus / Ragulator complex / ATP export / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / endocytic recycling / Negative regulators of DDX58/IFIH1 signaling / rRNA primary transcript binding ...positive regulation of RNA import into nucleus / Ragulator complex / ATP export / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / endocytic recycling / Negative regulators of DDX58/IFIH1 signaling / rRNA primary transcript binding / positive regulation of translational fidelity / Protein methylation / RMTs methylate histone arginines / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / nonfunctional rRNA decay / U3 snoRNA binding / response to osmotic stress / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / poly(A)+ mRNA export from nucleus / preribosome, small subunit precursor / snoRNA binding / mRNA destabilization / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / regulation of cellular amino acid metabolic process / proteasome assembly / G-protein alpha-subunit binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / regulation of translational fidelity / Ub-specific processing proteases / ribosomal subunit export from nucleus / translation regulator activity / ribonucleoprotein complex binding / ribosomal small subunit export from nucleus / 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) / DNA-(apurinic or apyrimidinic site) endonuclease activity / rescue of stalled ribosome / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / translational initiation / protein kinase C binding / maintenance of translational fidelity / cytoplasmic stress granule / rRNA processing / unfolded protein binding / protein transport / late endosome / ribosome biogenesis / ribosome binding / late endosome membrane / ribosomal small subunit biogenesis / ribosomal small subunit assembly / cellular response to oxidative stress / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / rRNA binding / non-specific serine/threonine protein kinase / negative regulation of translation / ribosome / protein kinase activity / structural constituent of ribosome / translation / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / GTPase activity / mRNA binding / nucleolus / GTP binding / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Scaiola A / Pena C / Weisser M / Boehringer D / Leibundgut M / Klingauf-Nerurkar P / Gerhardy S / Panse VG / Ban N | |||||||||
Citation | Journal: EMBO J / Year: 2018 Title: Structure of a eukaryotic cytoplasmic pre-40S ribosomal subunit. Authors: Alain Scaiola / Cohue Peña / Melanie Weisser / Daniel Böhringer / Marc Leibundgut / Purnima Klingauf-Nerurkar / Stefan Gerhardy / Vikram Govind Panse / Nenad Ban / Abstract: Final maturation of eukaryotic ribosomes occurs in the cytoplasm and requires the sequential removal of associated assembly factors and processing of the immature 20S pre-RNA Using cryo-electron ...Final maturation of eukaryotic ribosomes occurs in the cytoplasm and requires the sequential removal of associated assembly factors and processing of the immature 20S pre-RNA Using cryo-electron microscopy (cryo-EM), we have determined the structure of a yeast cytoplasmic pre-40S particle in complex with Enp1, Ltv1, Rio2, Tsr1, and Pno1 assembly factors poised to initiate final maturation. The structure reveals that the pre-rRNA adopts a highly distorted conformation of its 3' major and 3' minor domains stabilized by the binding of the assembly factors. This observation is consistent with a mechanism that involves concerted release of the assembly factors orchestrated by the folding of the rRNA in the head of the pre-40S subunit during the final stages of maturation. Our results provide a structural framework for the coordination of the final maturation events that drive a pre-40S particle toward the mature form capable of engaging in translation. | |||||||||
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_4214.map.gz | 11.4 MB | EMDB map data format | |
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Header (meta data) | emd-4214-v30.xml emd-4214.xml | 54.2 KB 54.2 KB | Display Display | EMDB header |
Images | emd_4214.png | 105.2 KB | ||
Filedesc metadata | emd-4214.cif.gz | 12.1 KB | ||
Others | emd_4214_half_map_1.map.gz emd_4214_half_map_2.map.gz | 98 MB 97.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4214 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4214 | HTTPS FTP |
-Validation report
Summary document | emd_4214_validation.pdf.gz | 347.6 KB | Display | EMDB validaton report |
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Full document | emd_4214_full_validation.pdf.gz | 346.7 KB | Display | |
Data in XML | emd_4214_validation.xml.gz | 12.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4214 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4214 | HTTPS FTP |
-Related structure data
Related structure data | 6faiMC 4215C 4216C 4217C 4218C C: citing same article (ref.) M: atomic model generated by this map |
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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_4214.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #1
File | emd_4214_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_4214_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Cytoplasmic pre-40S ribosomal subunit
+Supramolecule #1: Cytoplasmic pre-40S ribosomal subunit
+Macromolecule #1: 40S ribosomal protein S27-A
+Macromolecule #2: 40S ribosomal protein S28-A
+Macromolecule #3: 40S ribosomal protein S29-A
+Macromolecule #4: 40S ribosomal protein S30-A
+Macromolecule #5: Guanine nucleotide-binding protein subunit beta-like protein
+Macromolecule #6: Pre-rRNA-processing protein PNO1
+Macromolecule #7: Essential nuclear protein 1
+Macromolecule #8: Protein LTV1
+Macromolecule #9: Ribosome biogenesis protein TSR1
+Macromolecule #10: Serine/threonine-protein kinase RIO2
+Macromolecule #12: 40S ribosomal protein S0-A
+Macromolecule #13: 40S ribosomal protein S1-A
+Macromolecule #14: 40S ribosomal protein S2
+Macromolecule #15: 40S ribosomal protein S3
+Macromolecule #16: 40S ribosomal protein S4-A
+Macromolecule #17: 40S ribosomal protein S5
+Macromolecule #18: 40S ribosomal protein S6-A
+Macromolecule #19: 40S ribosomal protein S7-A
+Macromolecule #20: 40S ribosomal protein S8-A
+Macromolecule #21: 40S ribosomal protein S9-A
+Macromolecule #22: 40S ribosomal protein S11-A
+Macromolecule #23: 40S ribosomal protein S12
+Macromolecule #24: 40S ribosomal protein S13
+Macromolecule #25: 40S ribosomal protein S14-A
+Macromolecule #26: 40S ribosomal protein S15
+Macromolecule #27: 40S ribosomal protein S16-A
+Macromolecule #28: 40S ribosomal protein S17-A
+Macromolecule #29: 40S ribosomal protein S18-A
+Macromolecule #30: 40S ribosomal protein S19-A
+Macromolecule #31: 40S ribosomal protein S20
+Macromolecule #32: 40S ribosomal protein S21-A
+Macromolecule #33: 40S ribosomal protein S22-A
+Macromolecule #34: 40S ribosomal protein S23-A
+Macromolecule #35: 40S ribosomal protein S24-A
+Macromolecule #36: 40S ribosomal protein S25-A
+Macromolecule #11: 20S ribosomal RNA
+Macromolecule #37: ZINC ION
+Macromolecule #38: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 40.0 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 |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 165168 |
Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |