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- EMDB-0374: Cryo-EM structure of Rpl10-inserted (RI) pre-60S ribosomal subunit -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0374 | ||||||||||||||||||
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Title | Cryo-EM structure of Rpl10-inserted (RI) pre-60S ribosomal subunit | ||||||||||||||||||
![]() | Cryo-EM structure of Rpl10-inserted (RI) pre-60S ribosomal subunit | ||||||||||||||||||
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Function / homology | ![]() ascospore wall assembly / protein tyrosine/serine/threonine phosphatase activity / preribosome binding / positive regulation of autophagosome assembly / mating projection tip / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cellular response to nitrogen starvation / 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 ...ascospore wall assembly / protein tyrosine/serine/threonine phosphatase activity / preribosome binding / positive regulation of autophagosome assembly / mating projection tip / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cellular response to nitrogen starvation / 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 / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / ribosomal large subunit binding / 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) / negative regulation of mRNA splicing, via spliceosome / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / translational elongation / ribosomal large subunit export from nucleus / protein-RNA complex assembly / regulation of translational fidelity / ribosomal subunit export from nucleus / translational termination / translation initiation factor activity / maturation of LSU-rRNA / protein-tyrosine-phosphatase / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit biogenesis / meiotic cell cycle / protein tyrosine phosphatase activity / translational initiation / macroautophagy / maintenance of translational fidelity / autophagy / modification-dependent protein catabolic process / cytoplasmic stress granule / rRNA processing / protein tag activity / protein transport / ribosome biogenesis / protein-macromolecule adaptor activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / translation / response to antibiotic / GTPase activity / mRNA binding / ubiquitin protein ligase binding / nucleolus / GTP binding / RNA binding / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||||||||
![]() | Zhou Y / Musalgaonkar S / Johnson AW / Taylor DW | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 201.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 65.1 KB 65.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.4 KB | Display | ![]() |
Images | ![]() | 174.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6n8oMC ![]() 0369C ![]() 0370C ![]() 0371C ![]() 0372C ![]() 0373C ![]() 6n8jC ![]() 6n8kC ![]() 6n8lC ![]() 6n8mC ![]() 6n8nC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of Rpl10-inserted (RI) 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
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Sample components
+Entire : Rpl10-inserted (RI) pre-60S ribosomal subunit
+Supramolecule #1: Rpl10-inserted (RI) pre-60S ribosomal subunit
+Macromolecule #1: Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), m...
+Macromolecule #2: 5S rRNA
+Macromolecule #3: 5.8S rRNA
+Macromolecule #4: Tyrosine-protein phosphatase YVH1
+Macromolecule #5: Eukaryotic translation initiation factor 6
+Macromolecule #6: Ribosomal protein L12
+Macromolecule #7: Large subunit GTPase 1
+Macromolecule #8: 60S ribosomal export protein NMD3
+Macromolecule #9: 60S ribosomal protein L2-A
+Macromolecule #10: 60S ribosomal protein L3
+Macromolecule #11: 60S ribosomal protein L4-A
+Macromolecule #12: 60S ribosomal protein L5
+Macromolecule #13: 60S ribosomal protein L6-A
+Macromolecule #14: 60S ribosomal protein L7-A
+Macromolecule #15: 60S ribosomal protein L8-A
+Macromolecule #16: 60S ribosomal protein L9-A
+Macromolecule #17: 60S ribosomal protein L10
+Macromolecule #18: 60S ribosomal protein L11-A
+Macromolecule #19: 60S ribosomal protein L13-A
+Macromolecule #20: 60S ribosomal protein L14-A
+Macromolecule #21: 60S ribosomal protein L42-A
+Macromolecule #22: 60S ribosomal protein L43-A
+Macromolecule #23: Ribosomal Protein uL1
+Macromolecule #24: 60S ribosomal protein L15-A
+Macromolecule #25: 60S ribosomal protein L16-A
+Macromolecule #26: 60S ribosomal protein L17-A
+Macromolecule #27: 60S ribosomal protein L18-A
+Macromolecule #28: 60S ribosomal protein L19-A
+Macromolecule #29: 60S ribosomal protein L20-A
+Macromolecule #30: 60S ribosomal protein L21-A
+Macromolecule #31: 60S ribosomal protein L22-A
+Macromolecule #32: 60S ribosomal protein L23-A
+Macromolecule #33: 60S ribosomal protein L24-A
+Macromolecule #34: 60S ribosomal protein L25
+Macromolecule #35: 60S ribosomal protein L26-A
+Macromolecule #36: 60S ribosomal protein L27-A
+Macromolecule #37: 60S ribosomal protein L28
+Macromolecule #38: 60S ribosomal protein L29
+Macromolecule #39: 60S ribosomal protein L30
+Macromolecule #40: 60S ribosomal protein L31-A
+Macromolecule #41: 60S ribosomal protein L32
+Macromolecule #42: 60S ribosomal protein L33-A
+Macromolecule #43: 60S ribosomal protein L34-A
+Macromolecule #44: 60S ribosomal protein L35-A
+Macromolecule #45: 60S ribosomal protein L36-A
+Macromolecule #46: 60S ribosomal protein L37-A
+Macromolecule #47: 60S ribosomal protein L38
+Macromolecule #48: 60S ribosomal protein L39
+Macromolecule #49: Ubiquitin-60S ribosomal protein L40
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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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 |
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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 exposure time: 6.0 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |