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- PDB-6ft6: Structure of the Nop53 pre-60S particle bound to the exosome nucl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ft6 | ||||||
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Title | Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors | ||||||
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![]() | RNA / RNA exosome / Ribosome / pre-ribosome / Mtr4 / Helicase | ||||||
Function / homology | ![]() nuclear mRNA surveillance of mRNA 3'-end processing / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / TRAMP complex / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent CUT catabolic process / protein-RNA complex remodeling / regulation of ribosomal subunit export from nucleus / TRAMP-dependent tRNA surveillance pathway / RNA fragment catabolic process ...nuclear mRNA surveillance of mRNA 3'-end processing / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / TRAMP complex / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent CUT catabolic process / protein-RNA complex remodeling / regulation of ribosomal subunit export from nucleus / TRAMP-dependent tRNA surveillance pathway / RNA fragment catabolic process / exosome (RNase complex) / nuclear polyadenylation-dependent rRNA catabolic process / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / nuclear exosome (RNase complex) / poly(A)-dependent snoRNA 3'-end processing / U4 snRNA 3'-end processing / 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 / histone mRNA catabolic process / nuclear mRNA surveillance / rRNA catabolic process / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / PeBoW complex / 7S RNA binding / poly(A) binding / rRNA primary transcript 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) / 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) / maturation of 5.8S rRNA / 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 / 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 / RNA processing / ribonucleoprotein complex binding / ribosomal subunit export from nucleus / enzyme regulator activity / 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) / Neutrophil degranulation / translation initiation factor activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear periphery / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / assembly of large subunit precursor of preribosome / maturation of LSU-rRNA / cytosolic ribosome assembly / ribosomal large subunit biogenesis / maturation of SSU-rRNA / macroautophagy / small-subunit processome / maintenance of translational fidelity / ribosomal large subunit assembly / mRNA processing / rRNA processing / metallopeptidase activity / double-stranded RNA binding / protein transport / ribosome biogenesis / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / ATPase binding / 5S rRNA binding / large ribosomal subunit rRNA binding / regulation of gene expression / double-stranded DNA binding / nucleic acid binding / cytosolic large ribosomal subunit / cytoplasmic translation / RNA helicase activity / oxidoreductase activity / single-stranded RNA binding / rRNA binding / negative regulation of translation / ribosome / RNA helicase / structural constituent of ribosome / translation / nucleotide binding / GTPase activity / mRNA binding / protein-containing complex binding / nucleolus / GTP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||
![]() | Schuller, J.M. / Falk, S. / Conti, E. | ||||||
Funding support | ![]()
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![]() | ![]() 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
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 3.4 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 290.4 KB | Display | |
Data in CIF | ![]() | 503.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4302MC ![]() 4301C ![]() 6fszC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-RNA chain , 3 types, 3 molecules 213
#1: RNA chain | Mass: 51999.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: GenBank: 1279395616 |
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#50: RNA chain | Mass: 1097493.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: GenBank: 834774822 |
#51: RNA chain | Mass: 38951.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: GenBank: 1329886537 |
+60S ribosomal protein ... , 35 types, 35 molecules ABCDEFGHJLMNOPQRSTUVXYZacdefgh...
-Protein , 9 types, 9 molecules Inswyz45MM
#10: Protein | Mass: 18546.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: Q08004 |
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#40: Protein | Mass: 69984.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P53261 |
#43: Protein | Mass: 57798.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P40010 |
#46: Protein | Mass: 23001.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: Q08746 |
#48: Protein | Mass: 26476.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: Q12522 |
#49: Protein | Mass: 12435.429 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P38202 |
#52: Protein | Mass: 65290.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: Q03862, Hydrolases |
#53: Protein | Mass: 14460.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P53188 |
#56: Protein | Mass: 115230.648 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: MTR4, DOB1, YJL050W, J1158 / Production host: ![]() ![]() |
-Ribosome assembly ... , 2 types, 2 molecules Wx
#23: Protein | Mass: 27098.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P33201 |
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#47: Protein | Mass: 57106.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P25382 |
-Nucleolar GTP-binding protein ... , 2 types, 2 molecules bm
#28: Protein | Mass: 74531.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: Q02892 |
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#39: Protein | Mass: 55585.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P53742 |
-Ribosome biogenesis protein ... , 3 types, 3 molecules ruv
#42: Protein | Mass: 29786.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P40078 |
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#44: Protein | Mass: 24027.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: Q07915 |
#45: Protein | Mass: 39665.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P36160 |
-Exosome complex ... , 2 types, 2 molecules KKLL
#54: Protein | Mass: 84160.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: RRP6, UNC733, YOR001W / Production host: ![]() ![]() References: UniProt: Q12149, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters |
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#55: Protein | Mass: 21086.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: LRP1, RRP47, YC1D, YHR081W / Production host: ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules NN
#57: Protein/peptide | Mass: 954.168 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() |
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-Non-polymers , 3 types, 8 molecules ![](data/chem/img/ZN.gif)
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#58: Chemical | ChemComp-ZN / #59: Chemical | #60: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: ![]() ![]() | ||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 38.4 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.13rc2_2986: / Classification: refinement |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22439 / Symmetry type: POINT |