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Yorodumi- EMDB-30170: Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30170 | |||||||||
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Title | Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.12 Angstroms resolution(state R1) | |||||||||
Map data | Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4%u220663-87 strain at 3.12 Angstroms resolution(state R1) | |||||||||
Sample |
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Function / homology | Function and homology information protein-RNA complex remodeling / regulation of ribosomal subunit export from nucleus / 7S RNA 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 / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of 5.8S rRNA / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit ...protein-RNA complex remodeling / regulation of ribosomal subunit export from nucleus / 7S RNA 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 / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 / nuclear-transcribed mRNA catabolic process / ATPase activator activity / 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 / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation initiation factor activity / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear periphery / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / macroautophagy / maintenance of translational fidelity / rRNA processing / ribosome biogenesis / ATPase binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / GTPase activity / mRNA binding / nucleolus / GTP binding / RNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) / Baker's yeast (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.12 Å | |||||||||
Authors | Li Y / Wilson DM | |||||||||
Funding support | United States, China, 2 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Structural insights into assembly of the ribosomal nascent polypeptide exit tunnel. Authors: Daniel M Wilson / Yu Li / Amber LaPeruta / Michael Gamalinda / Ning Gao / John L Woolford / Abstract: The nascent polypeptide exit tunnel (NPET) is a major functional center of 60S ribosomal subunits. However, little is known about how the NPET is constructed during ribosome assembly. We utilized ...The nascent polypeptide exit tunnel (NPET) is a major functional center of 60S ribosomal subunits. However, little is known about how the NPET is constructed during ribosome assembly. We utilized molecular genetics, biochemistry, and cryo-electron microscopy (cryo-EM) to investigate the functions of two NPET-associated proteins, ribosomal protein uL4 and assembly factor Nog1, in NPET assembly. Structures of mutant pre-ribosomes lacking the tunnel domain of uL4 reveal a misassembled NPET, including an aberrantly flexible ribosomal RNA helix 74, resulting in at least three different blocks in 60S assembly. Structures of pre-ribosomes lacking the C-terminal extension of Nog1 demonstrate that this extension scaffolds the tunnel domain of uL4 in the NPET to help maintain stability in the core of pre-60S subunits. Our data reveal that uL4 and Nog1 work together in the maturation of ribosomal RNA helix 74, which is required to ensure proper construction of the NPET and 60S ribosomal subunits. | |||||||||
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_30170.map.gz | 96.4 MB | EMDB map data format | |
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Header (meta data) | emd-30170-v30.xml emd-30170.xml | 57.1 KB 57.1 KB | Display Display | EMDB header |
Images | emd_30170.png | 65.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30170 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30170 | HTTPS FTP |
-Validation report
Summary document | emd_30170_validation.pdf.gz | 577 KB | Display | EMDB validaton report |
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Full document | emd_30170_full_validation.pdf.gz | 576.5 KB | Display | |
Data in XML | emd_30170_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | emd_30170_validation.cif.gz | 7.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30170 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30170 | HTTPS FTP |
-Related structure data
Related structure data | 7bt6MC 7btbC M: atomic model generated by this map C: citing same article (ref.) |
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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_30170.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4%u220663-87 strain at 3.12 Angstroms resolution(state R1) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.3734 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 : Eukaryotic pre-60S ribosomal subunits from Saccharomyces cerevisi...
+Supramolecule #1: Eukaryotic pre-60S ribosomal subunits from Saccharomyces cerevisi...
+Macromolecule #1: 60S ribosomal protein L2-A
+Macromolecule #2: 60S ribosomal protein L3
+Macromolecule #3: 60S ribosomal protein L4-A
+Macromolecule #4: 60S ribosomal protein L5
+Macromolecule #5: 60S ribosomal protein L6-A
+Macromolecule #6: 60S ribosomal protein L7-A
+Macromolecule #7: 60S ribosomal protein L8-A
+Macromolecule #8: 60S ribosomal protein L9-A
+Macromolecule #9: 60S ribosomal protein L11-A
+Macromolecule #10: 60S ribosomal protein L13-A
+Macromolecule #11: 60S ribosomal protein L14-A
+Macromolecule #12: 60S ribosomal protein L15-A
+Macromolecule #13: 60S ribosomal protein L16-A
+Macromolecule #14: 60S ribosomal protein L17-A
+Macromolecule #15: 60S ribosomal protein L18-A
+Macromolecule #16: 60S ribosomal protein L19-A
+Macromolecule #17: 60S ribosomal protein L20-A
+Macromolecule #18: 60S ribosomal protein L21-A
+Macromolecule #19: 60S ribosomal protein L22-A
+Macromolecule #20: 60S ribosomal protein L23-A
+Macromolecule #21: Ribosome assembly factor MRT4
+Macromolecule #22: 60S ribosomal protein L25
+Macromolecule #23: 60S ribosomal protein L26-A
+Macromolecule #24: 60S ribosomal protein L27-A
+Macromolecule #25: 60S ribosomal protein L28
+Macromolecule #26: Nucleolar GTP-binding protein 1
+Macromolecule #27: 60S ribosomal protein L30
+Macromolecule #28: 60S ribosomal protein L31-A
+Macromolecule #29: 60S ribosomal protein L32
+Macromolecule #30: 60S ribosomal protein L33-A
+Macromolecule #31: 60S ribosomal protein L34-A
+Macromolecule #32: 60S ribosomal protein L35-A
+Macromolecule #33: 60S ribosomal protein L36-A
+Macromolecule #34: 60S ribosomal protein L37-A
+Macromolecule #35: 60S ribosomal protein L38
+Macromolecule #36: Nucleolar GTP-binding protein 2
+Macromolecule #37: 60S ribosomal protein L43-A
+Macromolecule #38: Ribosome biogenesis protein NSA2
+Macromolecule #39: Ribosome biogenesis protein RLP24
+Macromolecule #40: Ribosome biogenesis protein RPF2
+Macromolecule #41: Regulator of ribosome biosynthesis
+Macromolecule #42: Ribosome assembly protein 4
+Macromolecule #43: Eukaryotic translation initiation factor 6
+Macromolecule #44: UPF0642 protein YBL028C
+Macromolecule #45: RDN25-1 rRNA
+Macromolecule #46: RDN5.8-1 rRNA
+Macromolecule #47: RDN5-2 rRNA
+Macromolecule #48: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #49: MAGNESIUM ION
+Macromolecule #50: ZINC 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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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.9 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 103319 |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |