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Yorodumi- EMDB-32794: Cryo-EM structure of a yeast pre-40S ribosomal subunit - State Ts... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32794 | |||||||||
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Title | Cryo-EM structure of a yeast pre-40S ribosomal subunit - State Tsr1-2 (with Rps2) | |||||||||
Map data | local resolution filtered | |||||||||
Sample |
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Keywords | ribosome biogenesis / 40S ribosome / RIBOSOME | |||||||||
Function / homology | Function and homology information 18S rRNA (guanine1575-N7)-methyltransferase / rRNA (guanine-N7)-methylation / tRNA methyltransferase complex / rRNA (guanine) methyltransferase activity / 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) / rRNA primary transcript binding / RMTs methylate histone arginines / positive regulation of translational fidelity / Protein methylation ...18S rRNA (guanine1575-N7)-methyltransferase / rRNA (guanine-N7)-methylation / tRNA methyltransferase complex / rRNA (guanine) methyltransferase activity / 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) / rRNA primary transcript binding / RMTs methylate histone arginines / positive regulation of translational fidelity / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / U3 snoRNA binding / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / preribosome, small subunit precursor / Ribosomal scanning and start codon recognition / 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 / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / proteasome assembly / 90S preribosome / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of translational fidelity / ribonucleoprotein complex binding / ribosomal subunit export from nucleus / 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) / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / maintenance of translational fidelity / cytoplasmic stress granule / rRNA processing / ribosomal small subunit biogenesis / unfolded protein binding / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosomal small subunit assembly / cytosolic small ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / translation / GTPase activity / mRNA binding / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Cheng J / Lau B / Thoms M / Ameismeier M / Berninghausen O / Hurt E / Beckmann R | |||||||||
Funding support | 1 items
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Citation | Journal: Nucleic Acids Res / Year: 2022 Title: The nucleoplasmic phase of pre-40S formation prior to nuclear export. Authors: Jingdong Cheng / Benjamin Lau / Matthias Thoms / Michael Ameismeier / Otto Berninghausen / Ed Hurt / Roland Beckmann / Abstract: Biogenesis of the small ribosomal subunit in eukaryotes starts in the nucleolus with the formation of a 90S precursor and ends in the cytoplasm. Here, we elucidate the enigmatic structural ...Biogenesis of the small ribosomal subunit in eukaryotes starts in the nucleolus with the formation of a 90S precursor and ends in the cytoplasm. Here, we elucidate the enigmatic structural transitions of assembly intermediates from human and yeast cells during the nucleoplasmic maturation phase. After dissociation of all 90S factors, the 40S body adopts a close-to-mature conformation, whereas the 3' major domain, later forming the 40S head, remains entirely immature. A first coordination is facilitated by the assembly factors TSR1 and BUD23-TRMT112, followed by re-positioning of RRP12 that is already recruited early to the 90S for further head rearrangements. Eventually, the uS2 cluster, CK1 (Hrr25 in yeast) and the export factor SLX9 associate with the pre-40S to provide export competence. These exemplary findings reveal the evolutionary conserved mechanism of how yeast and humans assemble the 40S ribosomal subunit, but reveal also a few minor differences. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32794.map.gz | 105.9 MB | EMDB map data format | |
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Header (meta data) | emd-32794-v30.xml emd-32794.xml | 31 KB 31 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_32794_fsc.xml | 12.8 KB | Display | FSC data file |
Images | emd_32794.png | 135.1 KB | ||
Filedesc metadata | emd-32794.cif.gz | 9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32794 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32794 | HTTPS FTP |
-Validation report
Summary document | emd_32794_validation.pdf.gz | 450.5 KB | Display | EMDB validaton report |
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Full document | emd_32794_full_validation.pdf.gz | 450.1 KB | Display | |
Data in XML | emd_32794_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | emd_32794_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32794 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32794 | HTTPS FTP |
-Related structure data
Related structure data | 7wtpMC 7wtnC 7wtoC 7wtqC 7wtrC 7wtsC 7wttC 7wtuC 7wtvC 7wtwC 7wtxC 7wtzC 7wu0C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_32794.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | local resolution filtered | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.059 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : Yeast pre-40S ribosomal subunit
+Supramolecule #1: Yeast pre-40S ribosomal subunit
+Macromolecule #1: 18S rRNA
+Macromolecule #2: 40S ribosomal protein S1-A
+Macromolecule #3: 40S ribosomal protein S2
+Macromolecule #4: 40S ribosomal protein S4-A
+Macromolecule #5: 40S ribosomal protein S6-A
+Macromolecule #6: 40S ribosomal protein S7-A
+Macromolecule #7: 40S ribosomal protein S8-A
+Macromolecule #8: 40S ribosomal protein S9-A
+Macromolecule #9: 40S ribosomal protein S11-A
+Macromolecule #10: 40S ribosomal protein S13
+Macromolecule #11: 40S ribosomal protein S14-A
+Macromolecule #12: 40S ribosomal protein S22-A
+Macromolecule #13: 40S ribosomal protein S23-A
+Macromolecule #14: 40S ribosomal protein S24-A
+Macromolecule #15: 40S ribosomal protein S27-A
+Macromolecule #16: 40S ribosomal protein S30-A
+Macromolecule #17: Pre-rRNA-processing protein PNO1
+Macromolecule #18: 18S rRNA (guanine(1575)-N(7))-methyltransferase
+Macromolecule #19: Ribosome biogenesis protein TSR1
+Macromolecule #20: ZINC 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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 44.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |