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Yorodumi- EMDB-4302: Structure of the Nop53 pre-60S particle bound to the exosome nucl... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4302 | |||||||||
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Title | Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors | |||||||||
Map data | Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors | |||||||||
Sample |
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Function / homology | Function and homology information nuclear mRNA surveillance of mRNA 3'-end processing / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / TRAMP complex / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / protein-RNA complex remodeling / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing ...nuclear mRNA surveillance of mRNA 3'-end processing / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / TRAMP complex / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / protein-RNA complex remodeling / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / regulation of ribosomal subunit export from nucleus / TRAMP-dependent tRNA surveillance pathway / RNA fragment catabolic process / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / exosome (RNase complex) / nuclear exosome (RNase complex) / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Hydrolases / 3'-5' RNA helicase activity / rRNA catabolic process / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / histone mRNA catabolic process / nuclear mRNA surveillance / PeBoW complex / Antigen processing: Ubiquitination & Proteasome degradation / 7S RNA binding / rRNA primary transcript binding / poly(A) binding / positive regulation of ATP-dependent activity / RNA catabolic process / 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) / maturation of 5.8S rRNA / ribosomal subunit export from nucleus / Major pathway of rRNA processing in the nucleolus and cytosol / 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 / 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) / regulation of translational fidelity / RNA processing / ribonucleoprotein complex binding / enzyme regulator activity / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / Neutrophil degranulation / translation initiation factor activity / nuclear periphery / small-subunit processome / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / maintenance of translational fidelity / macroautophagy / ribosomal large subunit assembly / mRNA processing / rRNA processing / metallopeptidase activity / large ribosomal subunit rRNA binding / protein transport / double-stranded RNA binding / ribosome biogenesis / cytoplasmic translation / 5S rRNA binding / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / cytosolic large ribosomal subunit / 3'-5'-RNA exonuclease activity / ATPase binding / double-stranded DNA binding / regulation of gene expression / negative regulation of translation / RNA helicase activity / single-stranded RNA binding / nucleic acid binding / rRNA binding / oxidoreductase activity / RNA helicase / ribosome / structural constituent of ribosome / translation / nucleotide binding / mRNA binding / GTPase activity / protein-containing complex binding / GTP binding 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: 3.9 Å | |||||||||
Authors | Schuller JM / Falk S / Conti E | |||||||||
Funding support | Belgium, 1 items
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Citation | Journal: Science / Year: 2018 Title: Structure of the nuclear exosome captured on a maturing preribosome. Authors: Jan Michael Schuller / Sebastian Falk / Lisa Fromm / Ed Hurt / Elena Conti / Abstract: The RNA exosome complex processes and degrades a wide range of transcripts, including ribosomal RNAs (rRNAs). We used cryo-electron microscopy to visualize the yeast nuclear exosome holocomplex ...The RNA exosome complex processes and degrades a wide range of transcripts, including ribosomal RNAs (rRNAs). We used cryo-electron microscopy to visualize the yeast nuclear exosome holocomplex captured on a precursor large ribosomal subunit (pre-60) during 7-to-5.8 rRNA processing. The cofactors of the nuclear exosome are sandwiched between the ribonuclease core complex (Exo-10) and the remodeled "foot" structure of the pre-60 particle, which harbors the 5.8 rRNA precursor. The exosome-associated helicase Mtr4 recognizes the preribosomal substrate by docking to specific sites on the 25 rRNA, captures the 3' extension of the 5.8 rRNA, and channels it toward Exo-10. The structure elucidates how the exosome forms a structural and functional unit together with its massive pre-60 substrate to process rRNA during ribosome maturation. | |||||||||
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_4302.map.gz | 260.4 MB | EMDB map data format | |
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Header (meta data) | emd-4302-v30.xml emd-4302.xml | 78.2 KB 78.2 KB | Display Display | EMDB header |
Images | emd_4302.png | 569 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4302 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4302 | HTTPS FTP |
-Related structure data
Related structure data | 6ft6MC 4301C 6fszC 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_4302.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 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 : Structure of the Nop53 pre-60S particle bound to the exosome nucl...
+Supramolecule #1: Structure of the Nop53 pre-60S particle bound to the exosome nucl...
+Supramolecule #2: pre-60S particle
+Supramolecule #3: exosome nuclear cofactors
+Macromolecule #1: 7S ribosomal RNA
+Macromolecule #50: 25S ribosomal RNA
+Macromolecule #51: 5S ribosomal RNA
+Macromolecule #2: 60S ribosomal protein L2-A
+Macromolecule #3: 60S ribosomal protein L3
+Macromolecule #4: 60S ribosomal protein L4-A
+Macromolecule #5: 60S ribosomal protein L5
+Macromolecule #6: 60S ribosomal protein L6-A
+Macromolecule #7: 60S ribosomal protein L7-A
+Macromolecule #8: 60S ribosomal protein L8-A
+Macromolecule #9: 60S ribosomal protein L9-A
+Macromolecule #10: Bud site selection protein 20
+Macromolecule #11: 60S ribosomal protein L11-A
+Macromolecule #12: 60S ribosomal protein L13-A
+Macromolecule #13: 60S ribosomal protein L14-A
+Macromolecule #14: 60S ribosomal protein L15-A
+Macromolecule #15: 60S ribosomal protein L16-A
+Macromolecule #16: 60S ribosomal protein L17-A
+Macromolecule #17: 60S ribosomal protein L18-A
+Macromolecule #18: 60S ribosomal protein L19-A
+Macromolecule #19: 60S ribosomal protein L20-A
+Macromolecule #20: 60S ribosomal protein L21-A
+Macromolecule #21: 60S ribosomal protein L22-A
+Macromolecule #22: 60S ribosomal protein L23-A
+Macromolecule #23: Ribosome assembly factor MRT4
+Macromolecule #24: 60S ribosomal protein L25
+Macromolecule #25: 60S ribosomal protein L26-A
+Macromolecule #26: 60S ribosomal protein L27-A
+Macromolecule #27: 60S ribosomal protein L28
+Macromolecule #28: Nucleolar GTP-binding protein 1
+Macromolecule #29: 60S ribosomal protein L30
+Macromolecule #30: 60S ribosomal protein L31-A
+Macromolecule #31: 60S ribosomal protein L32
+Macromolecule #32: 60S ribosomal protein L33-A
+Macromolecule #33: 60S ribosomal protein L34-A
+Macromolecule #34: 60S ribosomal protein L35-A
+Macromolecule #35: 60S ribosomal protein L36-A
+Macromolecule #36: 60S ribosomal protein L37-A
+Macromolecule #37: 60S ribosomal protein L38
+Macromolecule #38: 60S ribosomal protein L39
+Macromolecule #39: Nucleolar GTP-binding protein 2
+Macromolecule #40: Pescadillo homolog
+Macromolecule #41: 60S ribosomal protein L43-A
+Macromolecule #42: Ribosome biogenesis protein NSA2
+Macromolecule #43: Nuclear GTP-binding protein NUG1
+Macromolecule #44: Ribosome biogenesis protein RLP24
+Macromolecule #45: Ribosome biogenesis protein RPF2
+Macromolecule #46: Regulator of ribosome biosynthesis
+Macromolecule #47: Ribosome assembly protein 4
+Macromolecule #48: Eukaryotic translation initiation factor 6
+Macromolecule #49: UPF0642 protein YBL028C
+Macromolecule #52: Probable metalloprotease ARX1
+Macromolecule #53: rRNA-processing protein CGR1
+Macromolecule #54: Exosome complex exonuclease RRP6
+Macromolecule #55: Exosome complex protein LRP1
+Macromolecule #56: ATP-dependent RNA helicase DOB1
+Macromolecule #57: MPP6
+Macromolecule #58: ZINC ION
+Macromolecule #59: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #60: 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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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 38.4 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: PROJECTION MATCHING |
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Final angle assignment | Type: PROJECTION MATCHING |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22439 |