+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0372 | ||||||||||||||||||
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Title | Cryo-EM structure of pre-Lsg1 (PL) pre-60S ribosomal subunit | ||||||||||||||||||
Map data | Cryo-EM structure of pre-Lsg1 (PL) pre-60S ribosomal subunit | ||||||||||||||||||
Sample |
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Function / homology | Function and homology information ascospore wall assembly / protein tyrosine/serine/threonine phosphatase activity / preribosome binding / positive regulation of autophagosome assembly / 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 ...ascospore wall assembly / protein tyrosine/serine/threonine phosphatase activity / preribosome binding / positive regulation of autophagosome assembly / 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 / 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 / meiotic cell cycle / ribosomal subunit export from nucleus / 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 / 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 / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol 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_0372.map.gz | 201.8 MB | EMDB map data format | |
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Header (meta data) | emd-0372-v30.xml emd-0372.xml | 62.5 KB 62.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0372_fsc.xml | 13.6 KB | Display | FSC data file |
Images | emd_0372.png | 161.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0372 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0372 | HTTPS FTP |
-Validation report
Summary document | emd_0372_validation.pdf.gz | 568.9 KB | Display | EMDB validaton report |
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Full document | emd_0372_full_validation.pdf.gz | 568.4 KB | Display | |
Data in XML | emd_0372_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | emd_0372_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0372 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0372 | HTTPS FTP |
-Related structure data
Related structure data | 6n8mMC 0369C 0370C 0371C 0373C 0374C 6n8jC 6n8kC 6n8lC 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_0372.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 pre-Lsg1 (PL) 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 : Pre-Lsg1 (PL) pre-60S ribosomal subunit
+Supramolecule #1: Pre-Lsg1 (PL) pre-60S ribosomal subunit
+Macromolecule #1: Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), m...
+Macromolecule #2: 5S rRNA
+Macromolecule #3: 5.8S RNA
+Macromolecule #4: Tyrosine-protein phosphatase YVH1
+Macromolecule #5: 60S ribosomal protein L2-A
+Macromolecule #6: 60S ribosomal protein L3
+Macromolecule #7: 60S ribosomal protein L4-A
+Macromolecule #8: 60S ribosomal protein L5
+Macromolecule #9: 60S ribosomal protein L6-A
+Macromolecule #10: 60S ribosomal protein L7-A
+Macromolecule #11: 60S ribosomal protein L8-A
+Macromolecule #12: 60S ribosomal protein L9-A
+Macromolecule #13: 60S ribosomal protein L11-A
+Macromolecule #14: 60S ribosomal protein L13-A
+Macromolecule #15: 60S ribosomal protein L14-A
+Macromolecule #16: 60S ribosomal protein L42-A
+Macromolecule #17: 60S ribosomal protein L43-A
+Macromolecule #18: Ribosomal Protein uL1
+Macromolecule #19: 60S ribosomal protein L15-A
+Macromolecule #20: 60S ribosomal protein L16-A
+Macromolecule #21: 60S ribosomal protein L17-A
+Macromolecule #22: 60S ribosomal protein L18-A
+Macromolecule #23: 60S ribosomal protein L19-A
+Macromolecule #24: 60S ribosomal protein L20-A
+Macromolecule #25: 60S ribosomal protein L21-A
+Macromolecule #26: 60S ribosomal protein L22-A
+Macromolecule #27: 60S ribosomal protein L23-A
+Macromolecule #28: 60S ribosomal protein L24-A
+Macromolecule #29: 60S ribosomal protein L25
+Macromolecule #30: 60S ribosomal protein L26-A
+Macromolecule #31: 60S ribosomal protein L27-A
+Macromolecule #32: 60S ribosomal protein L28
+Macromolecule #33: 60S ribosomal protein L29
+Macromolecule #34: 60S ribosomal protein L30
+Macromolecule #35: 60S ribosomal protein L31-A
+Macromolecule #36: 60S ribosomal protein L32
+Macromolecule #37: 60S ribosomal protein L33-A
+Macromolecule #38: 60S ribosomal protein L34-A
+Macromolecule #39: 60S ribosomal protein L35-A
+Macromolecule #40: 60S ribosomal protein L36-A
+Macromolecule #41: 60S ribosomal protein L37-A
+Macromolecule #42: 60S ribosomal protein L38
+Macromolecule #43: 60S ribosomal protein L39
+Macromolecule #44: Ubiquitin-60S ribosomal protein L40
+Macromolecule #45: 60S ribosomal export protein NMD3
+Macromolecule #46: Ribosomal protein L12
+Macromolecule #47: Eukaryotic translation initiation factor 6
-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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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: FIELD EMISSION GUN |
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 |