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Yorodumi- EMDB-0369: Cryo-EM structure of late nuclear (LN) pre-60S ribosomal subunit -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0369 | ||||||||||||||||||
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Title | Cryo-EM structure of late nuclear (LN) pre-60S ribosomal subunit | ||||||||||||||||||
Map data | Cryo-EM structure of late nuclear pre-60S ribosomal subunit | ||||||||||||||||||
Sample |
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Function / homology | Function and homology information regulation of ribosomal subunit export from nucleus / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear-transcribed mRNA catabolic process / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to cycloheximide / maturation of 5.8S rRNA / ribosomal subunit export from nucleus / SRP-dependent cotranslational protein targeting to membrane ...regulation of ribosomal subunit export from nucleus / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear-transcribed mRNA catabolic process / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to cycloheximide / maturation of 5.8S rRNA / ribosomal subunit export from nucleus / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / ATPase activator activity / Formation of a pool of free 40S subunits / ribosomal large subunit binding / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of mRNA splicing, via spliceosome / protein-RNA complex assembly / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit export from nucleus / regulation of translational fidelity / maturation of SSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / translation initiation factor activity / small-subunit processome / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / maintenance of translational fidelity / macroautophagy / rRNA processing / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / ribosome biogenesis / 5S rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / ATPase binding / negative regulation of translation / nucleic acid binding / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / GTPase activity / GTP binding / nucleolus / RNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Baker's yeast (brewer's yeast) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||||||||
Authors | Zhou Y / Musalgaonkar S / Johnson AW / Taylor DW | ||||||||||||||||||
Funding support | United States, 5 items
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Citation | Journal: Nat Commun / Year: 2019 Title: Tightly-orchestrated rearrangements govern catalytic center assembly of the ribosome. Authors: Yi Zhou / Sharmishtha Musalgaonkar / Arlen W Johnson / David W Taylor / Abstract: The catalytic activity of the ribosome is mediated by RNA, yet proteins are essential for the function of the peptidyl transferase center (PTC). In eukaryotes, final assembly of the PTC occurs in the ...The catalytic activity of the ribosome is mediated by RNA, yet proteins are essential for the function of the peptidyl transferase center (PTC). In eukaryotes, final assembly of the PTC occurs in the cytoplasm by insertion of the ribosomal protein Rpl10 (uL16). We determine structures of six intermediates in late nuclear and cytoplasmic maturation of the large subunit that reveal a tightly-choreographed sequence of protein and RNA rearrangements controlling the insertion of Rpl10. We also determine the structure of the biogenesis factor Yvh1 and show how it promotes assembly of the P stalk, a critical element for recruitment of GTPases that drive translation. Together, our structures provide a blueprint for final assembly of a functional ribosome. | ||||||||||||||||||
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_0369.map.gz | 201.1 MB | EMDB map data format | |
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Header (meta data) | emd-0369-v30.xml emd-0369.xml | 64.9 KB 64.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0369_fsc.xml | 13.5 KB | Display | FSC data file |
Images | emd_0369.png | 185.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0369 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0369 | HTTPS FTP |
-Related structure data
Related structure data | 6n8jMC 0370C 0371C 0372C 0373C 0374C 6n8kC 6n8lC 6n8mC 6n8nC 6n8oC 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_0369.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of late nuclear pre-60S ribosomal subunit | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Late nuclear (LN) pre-60S ribosomal subunit
+Supramolecule #1: Late nuclear (LN) pre-60S ribosomal subunit
+Macromolecule #1: 60S ribosomal protein L5
+Macromolecule #2: 60S ribosomal protein L11-A
+Macromolecule #3: 60S ribosomal protein L2-A
+Macromolecule #4: 60S ribosomal protein L28
+Macromolecule #5: 60S ribosomal protein L3
+Macromolecule #6: Nucleolar GTP-binding protein 1
+Macromolecule #7: 60S ribosomal protein L4-A
+Macromolecule #8: 60S ribosomal protein L30
+Macromolecule #9: 60S ribosomal protein L31-A
+Macromolecule #10: 60S ribosomal protein L6-A
+Macromolecule #11: 60S ribosomal protein L32
+Macromolecule #12: 60S ribosomal protein L7-A
+Macromolecule #13: 60S ribosomal protein L33-A
+Macromolecule #14: 60S ribosomal protein L8-A
+Macromolecule #15: 60S ribosomal protein L34-A
+Macromolecule #16: Bud site selection protein 20
+Macromolecule #17: 60S ribosomal protein L9-A
+Macromolecule #18: 60S ribosomal protein L35-A
+Macromolecule #19: 60S ribosomal protein L36-A
+Macromolecule #20: 60S ribosomal protein L37-A
+Macromolecule #21: 60S ribosomal protein L38
+Macromolecule #22: Nucleolar GTP-binding protein 2
+Macromolecule #23: 60S ribosomal protein L13-A
+Macromolecule #24: 60S ribosomal protein L39
+Macromolecule #25: 60S ribosomal protein L14-A
+Macromolecule #26: 60S ribosomal protein L43-A
+Macromolecule #27: 60S ribosomal protein L15-A
+Macromolecule #28: Ribosome biogenesis protein RLP24
+Macromolecule #29: 60S ribosomal protein L16-A
+Macromolecule #30: 60S ribosomal protein L17-A
+Macromolecule #31: 60S ribosomal protein L18-A
+Macromolecule #32: 60S ribosomal protein L19-A
+Macromolecule #33: Ribosome biogenesis protein NSA2
+Macromolecule #34: 60S ribosomal protein L20-A
+Macromolecule #35: 60S ribosomal protein L21-A
+Macromolecule #36: 60S ribosomal protein L22-A
+Macromolecule #37: 60S ribosomal protein L23-A
+Macromolecule #38: Ribosome assembly factor MRT4
+Macromolecule #39: 60S ribosomal protein L25
+Macromolecule #40: 60S ribosomal protein L26-A
+Macromolecule #41: Eukaryotic translation initiation factor 6
+Macromolecule #42: 60S ribosomal protein L27-A
+Macromolecule #43: UPF0642 protein YBL028C
+Macromolecule #44: 60S ribosomal protein L12
+Macromolecule #45: 60S ribosomal protein L42-A
+Macromolecule #46: 60S ribosomal protein L29
+Macromolecule #47: Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), m...
+Macromolecule #48: 5S rRNA
+Macromolecule #49: 5.8S rRNA
+Macromolecule #50: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #51: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Support film - Material: CARBON / Support film - topology: HOLEY / Details: unspecified |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 6.0 sec. / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |