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Yorodumi- EMDB-32792: Cryo-EM structure of a yeast pre-40S ribosomal subunit - State Ts... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32792 | |||||||||
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Title | Cryo-EM structure of a yeast pre-40S ribosomal subunit - State Tsr1-1 (with Rps2) | |||||||||
Map data | local resolution filtered | |||||||||
Sample |
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Function / homology | Function and homology information 18S rRNA (guanine1575-N7)-methyltransferase / rRNA (guanine-N7)-methylation / tRNA methyltransferase complex / rRNA (guanine) methyltransferase activity / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Protein methylation / RMTs methylate histone arginines / positive regulation of translational fidelity / mTORC1-mediated signalling / Protein hydroxylation ...18S rRNA (guanine1575-N7)-methyltransferase / rRNA (guanine-N7)-methylation / tRNA methyltransferase complex / rRNA (guanine) methyltransferase activity / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Protein methylation / RMTs methylate histone arginines / positive regulation of translational fidelity / mTORC1-mediated signalling / Protein hydroxylation / : / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / 90S preribosome / 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) / ribosomal small subunit export from nucleus / L13a-mediated translational silencing of Ceruloplasmin expression / proteasome assembly / 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) / regulation of translational fidelity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / maintenance of translational fidelity / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA processing / cytoplasmic stress granule / cytosolic small ribosomal subunit / unfolded protein binding / ribosome biogenesis / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / translation / mRNA binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / baker's yeast (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 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_32792.map.gz | 105.6 MB | EMDB map data format | |
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Header (meta data) | emd-32792-v30.xml emd-32792.xml | 28 KB 28 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_32792_fsc.xml | 12.8 KB | Display | FSC data file |
Images | emd_32792.png | 116.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32792 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32792 | HTTPS FTP |
-Related structure data
Related structure data | 7wtnMC 7wtoC 7wtpC 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_32792.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | local resolution filtered | ||||||||||||||||||||
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: 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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 44.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |