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- EMDB-0371: Cryo-EM structure of early cytoplasmic-late (ECL) pre-60S ribosom... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0371 | ||||||||||||||||||
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Title | Cryo-EM structure of early cytoplasmic-late (ECL) pre-60S ribosomal subunit | ||||||||||||||||||
![]() | Cryo-EM structure of early cytoplasmic-late (ECL) pre-60S ribosomal subunit | ||||||||||||||||||
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Function / homology | ![]() positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / pre-mRNA 5'-splice site binding / nuclear-transcribed mRNA catabolic process / 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 ...positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / pre-mRNA 5'-splice site binding / nuclear-transcribed mRNA catabolic process / 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 / ATPase activator activity / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / ribosomal large subunit export from nucleus / protein-RNA complex assembly / regulation of translational fidelity / ribosomal subunit export from nucleus / translation initiation factor activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / assembly of large subunit precursor of preribosome / maturation of LSU-rRNA / ribosomal large subunit biogenesis / cytosolic ribosome assembly / maturation of SSU-rRNA / small-subunit processome / macroautophagy / maintenance of translational fidelity / ribosomal large subunit assembly / rRNA processing / protein transport / ribosome biogenesis / ATPase binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / nucleic acid binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / GTPase activity / mRNA binding / nucleolus / GTP binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 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 | ![]() | 203 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 63.5 KB 63.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.3 KB | Display | ![]() |
Images | ![]() | 171.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 597.2 KB | Display | ![]() |
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Full document | ![]() | 596.8 KB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 18.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6n8lMC ![]() 0369C ![]() 0370C ![]() 0372C ![]() 0373C ![]() 0374C ![]() 6n8jC ![]() 6n8kC ![]() 6n8mC ![]() 6n8nC ![]() 6n8oC 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
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Annotation | Cryo-EM structure of early cytoplasmic-late (ECL) 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 : Early cytoplasmic-late (ECL) pre-60S ribosomal subunit
+Supramolecule #1: Early cytoplasmic-late (ECL) pre-60S ribosomal subunit
+Macromolecule #1: 60S ribosomal export protein NMD3
+Macromolecule #2: Ribosomal Protein uL1
+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: 60S ribosomal protein L13-A
+Macromolecule #23: 60S ribosomal protein L39
+Macromolecule #24: 60S ribosomal protein L14-A
+Macromolecule #25: 60S ribosomal protein L43-A
+Macromolecule #26: 60S ribosomal protein L15-A
+Macromolecule #27: Ribosome biogenesis protein RLP24
+Macromolecule #28: 60S ribosomal protein L16-A
+Macromolecule #29: 60S ribosomal protein L17-A
+Macromolecule #30: 60S ribosomal protein L18-A
+Macromolecule #31: 60S ribosomal protein L19-A
+Macromolecule #32: 60S ribosomal protein L20-A
+Macromolecule #33: 60S ribosomal protein L21-A
+Macromolecule #34: 60S ribosomal protein L22-A
+Macromolecule #35: 60S ribosomal protein L23-A
+Macromolecule #36: Ribosome assembly factor MRT4
+Macromolecule #37: 60S ribosomal protein L25
+Macromolecule #38: 60S ribosomal protein L26-A
+Macromolecule #39: Eukaryotic translation initiation factor 6
+Macromolecule #40: 60S ribosomal protein L27-A
+Macromolecule #41: UPF0642 protein YBL028C
+Macromolecule #42: 60S ribosomal protein L5
+Macromolecule #43: 60S ribosomal protein L11-A
+Macromolecule #44: 60S ribosomal protein L42-A
+Macromolecule #45: 60S ribosomal protein L29
+Macromolecule #46: Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), m...
+Macromolecule #47: 5S rRNA
+Macromolecule #48: 5.8S rRNA
-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 |