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Yorodumi- EMDB-34284: Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cere... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34284 | |||||||||
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Title | Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae (Rcl1/Cms1 KO) | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.7 Å | |||||||||
Authors | Cheng J / Lau B / Hurt E / Beckmann R | |||||||||
Funding support | 1 items
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Citation | Journal: Cell Rep / Year: 2022 Title: Cms1 coordinates stepwise local 90S pre-ribosome assembly with timely snR83 release. Authors: Benjamin Lau / Olga Beine-Golovchuk / Markus Kornprobst / Jingdong Cheng / Dieter Kressler / Beáta Jády / Tamás Kiss / Roland Beckmann / Ed Hurt / Abstract: Ribosome synthesis begins in the nucleolus with 90S pre-ribosome construction, but little is known about how the many different snoRNAs that modify the pre-rRNA are timely guided to their target ...Ribosome synthesis begins in the nucleolus with 90S pre-ribosome construction, but little is known about how the many different snoRNAs that modify the pre-rRNA are timely guided to their target sites. Here, we report a role for Cms1 in such a process. Initially, we discovered CMS1 as a null suppressor of a nop14 mutant impaired in Rrp12-Enp1 factor recruitment to the 90S. Further investigations detected Cms1 at the 18S rRNA 3' major domain of an early 90S that carried H/ACA snR83, which is known to guide pseudouridylation at two target sites within the same subdomain. Cms1 co-precipitates with many 90S factors, but Rrp12-Enp1 encircling the 3' major domain in the mature 90S is decreased. We suggest that Cms1 associates with the 3' major domain during early 90S biogenesis to restrict premature Rrp12-Enp1 binding but allows snR83 to timely perform its modification role before the next 90S assembly steps coupled with Cms1 release take place. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34284.map.gz | 32 MB | EMDB map data format | |
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Header (meta data) | emd-34284-v30.xml emd-34284.xml | 11.5 KB 11.5 KB | Display Display | EMDB header |
Images | emd_34284.png | 141.8 KB | ||
Others | emd_34284_half_map_1.map.gz emd_34284_half_map_2.map.gz | 391.2 MB 391.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34284 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34284 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_34284.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.045 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_34284_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34284_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : 90S pre-ribosome
Entire | Name: 90S pre-ribosome |
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Components |
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-Supramolecule #1: 90S pre-ribosome
Supramolecule | Name: 90S pre-ribosome / type: complex / Chimera: Yes / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-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: 3.5 µm / Nominal defocus min: 1.2 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 44.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: OTHER / Details: Relion |
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Final angle assignment | Type: OTHER / Details: Relion |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 16024 |