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- EMDB-32803: Cryo-EM structure of a human pre-40S ribosomal subunit - State RR... -
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Open data
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Basic information
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Title | Cryo-EM structure of a human pre-40S ribosomal subunit - State RRP12-A3 | |||||||||
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Function / homology | ![]() peptidyl-glutamine methylation / regulation of protein localization to nucleolus / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / rRNA (guanine) methyltransferase activity / tRNA modification in the nucleus and cytosol / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
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Method | ![]() ![]() | |||||||||
![]() | Cheng J / Lau B / Thoms M / Ameismeier M / Berninghausen O / Hurt E / Beckmann R | |||||||||
Funding support | 1 items
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![]() | ![]() 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 | ![]() | 106.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 48.1 KB 48.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.8 KB | Display | ![]() |
Images | ![]() | 154.5 KB | ||
Others | ![]() ![]() | 105.6 MB 71.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7wtwMC ![]() 7wtnC ![]() 7wtoC ![]() 7wtpC ![]() 7wtqC ![]() 7wtrC ![]() 7wtsC ![]() 7wttC ![]() 7wtuC ![]() 7wtvC ![]() 7wtxC ![]() 7wtzC ![]() 7wu0C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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
-Additional map: #2
File | emd_32803_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_32803_additional_2.map | ||||||||||||
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Density Histograms |
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Sample components
+Entire : Yeast pre-40S ribosomal subunit
+Supramolecule #1: Yeast pre-40S ribosomal subunit
+Macromolecule #1: 18S rRNA
+Macromolecule #2: 40S ribosomal protein S17
+Macromolecule #3: 40S ribosomal protein S27
+Macromolecule #4: 40S ribosomal protein S3a
+Macromolecule #5: 40S ribosomal protein S28
+Macromolecule #6: 40S ribosomal protein S4, X isoform
+Macromolecule #7: 40S ribosomal protein S30
+Macromolecule #8: 40S ribosomal protein S5
+Macromolecule #9: 40S ribosomal protein S7
+Macromolecule #10: 40S ribosomal protein S6
+Macromolecule #11: 40S ribosomal protein S25
+Macromolecule #12: 40S ribosomal protein S24
+Macromolecule #13: RNA-binding protein PNO1
+Macromolecule #14: 40S ribosomal protein S23
+Macromolecule #15: Bystin
+Macromolecule #16: Protein LTV1 homolog
+Macromolecule #17: 40S ribosomal protein S15a
+Macromolecule #18: Pre-rRNA-processing protein TSR1 homolog
+Macromolecule #19: 40S ribosomal protein S19
+Macromolecule #20: 40S ribosomal protein S18
+Macromolecule #21: 40S ribosomal protein S16
+Macromolecule #22: 40S ribosomal protein S15
+Macromolecule #23: 40S ribosomal protein S14
+Macromolecule #24: 40S ribosomal protein S13
+Macromolecule #25: 40S ribosomal protein S11
+Macromolecule #26: 40S ribosomal protein S9
+Macromolecule #27: 40S ribosomal protein S8
+Macromolecule #28: Multifunctional methyltransferase subunit TRM112-like protein
+Macromolecule #29: Probable 18S rRNA (guanine-N(7))-methyltransferase
+Macromolecule #30: RRP12-like protein
+Macromolecule #31: 40S ribosomal protein S12
+Macromolecule #32: Ubiquitin-40S ribosomal protein S27a
+Macromolecule #33: Ribosome biogenesis protein SLX9 homolog
+Macromolecule #34: 40S ribosomal protein SA
+Macromolecule #35: 40S ribosomal protein S2
+Macromolecule #36: 40S ribosomal protein S21
+Macromolecule #37: RNA-binding protein NOB1
+Macromolecule #38: ZINC ION
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
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 |