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Yorodumi- PDB-7ajt: Cryo-EM structure of the 90S-exosome super-complex (state Pre-A1-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ajt | ||||||
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Title | Cryo-EM structure of the 90S-exosome super-complex (state Pre-A1-exosome) | ||||||
Components |
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Keywords | RIBOSOME / Ribosome biogenesis / Exosome / 90S pre-ribosome / A1 cleavage / Mtr4 | ||||||
Function / homology | Function and homology information nuclear mRNA surveillance of mRNA 3'-end processing / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / TRAMP complex / mRNA modification / Noc4p-Nop14p complex / mRNA decay by 3' to 5' exoribonuclease / rRNA acetylation involved in maturation of SSU-rRNA / rRNA cytidine N-acetyltransferase activity / nuclear polyadenylation-dependent CUT catabolic process ...nuclear mRNA surveillance of mRNA 3'-end processing / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / TRAMP complex / mRNA modification / Noc4p-Nop14p complex / mRNA decay by 3' to 5' exoribonuclease / rRNA acetylation involved in maturation of SSU-rRNA / rRNA cytidine N-acetyltransferase activity / nuclear polyadenylation-dependent CUT catabolic process / regulatory ncRNA 3'-end processing / tRNA acetylation / box H/ACA snoRNA binding / regulation of ribosomal protein gene transcription by RNA polymerase II / TRAMP-dependent tRNA surveillance pathway / rRNA small subunit pseudouridine methyltransferase Nep1 / cytoplasmic exosome (RNase complex) / U1 snRNA 3'-end processing / RNA fragment catabolic process / CUT catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / rRNA 2'-O-methylation / nuclear polyadenylation-dependent rRNA catabolic process / Pwp2p-containing subcomplex of 90S preribosome / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / U4 snRNA 3'-end processing / exosome (RNase complex) / CURI complex / poly(A)-dependent snoRNA 3'-end processing / nuclear exosome (RNase complex) / histone H2AQ104 methyltransferase activity / nuclear microtubule / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / : / t-UTP complex / UTP-C complex / Mpp10 complex / snoRNA guided rRNA 2'-O-methylation / rRNA (pseudouridine) methyltransferase activity / nuclear-transcribed mRNA catabolic process, non-stop decay / rRNA modification / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of rRNA processing / : / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D sno(s)RNA binding / 3'-5' RNA helicase activity / snRNA binding / box C/D sno(s)RNA 3'-end processing / positive regulation of RNA binding / septum digestion after cytokinesis / rRNA catabolic process / nuclear mRNA surveillance / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rDNA heterochromatin / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / tRNA export from nucleus / rRNA methyltransferase activity / nonfunctional rRNA decay / regulation of transcription by RNA polymerase I / positive regulation of rRNA processing / single-stranded telomeric DNA binding / U4/U6 snRNP / rRNA base methylation / 90S preribosome assembly / rRNA primary transcript binding / poly(A) binding / SUMOylation of RNA binding proteins / Negative regulators of DDX58/IFIH1 signaling / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / O-methyltransferase activity / sno(s)RNA-containing ribonucleoprotein complex / protein localization to nucleolus / U4 snRNA binding / box C/D methylation guide snoRNP complex / mTORC1-mediated signalling / Protein hydroxylation / RNA catabolic process / rRNA methylation / poly(U) RNA binding / U4 snRNP / U3 snoRNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / poly(A)+ mRNA export from nucleus / rRNA metabolic process / maturation of 5.8S rRNA / establishment of cell polarity / snoRNA binding / precatalytic spliceosome / positive regulation of transcription by RNA polymerase I / spliceosomal complex assembly / 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 / nucleolar large rRNA transcription by RNA polymerase I Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Saccharomyces cerevisiae S288C (yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å | ||||||
Authors | Cheng, J. / Lau, B. / Flemming, D. / Venuta, G.L. / Berninghausen, O. / Beckmann, R. / Hurt, E. | ||||||
Citation | Journal: Mol Cell / Year: 2021 Title: Structure of the Maturing 90S Pre-ribosome in Association with the RNA Exosome. Authors: Benjamin Lau / Jingdong Cheng / Dirk Flemming / Giuseppe La Venuta / Otto Berninghausen / Roland Beckmann / Ed Hurt / Abstract: Ribosome assembly is catalyzed by numerous trans-acting factors and coupled with irreversible pre-rRNA processing, driving the pathway toward mature ribosomal subunits. One decisive step early in ...Ribosome assembly is catalyzed by numerous trans-acting factors and coupled with irreversible pre-rRNA processing, driving the pathway toward mature ribosomal subunits. One decisive step early in this progression is removal of the 5' external transcribed spacer (5'-ETS), an RNA extension at the 18S rRNA that is integrated into the huge 90S pre-ribosome structure. Upon endo-nucleolytic cleavage at an internal site, A, the 5'-ETS is separated from the 18S rRNA and degraded. Here we present biochemical and cryo-electron microscopy analyses that depict the RNA exosome, a major 3'-5' exoribonuclease complex, in a super-complex with the 90S pre-ribosome. The exosome is docked to the 90S through its co-factor Mtr4 helicase, a processive RNA duplex-dismantling helicase, which strategically positions the exosome at the base of 5'-ETS helices H9-H9', which are dislodged in our 90S-exosome structures. These findings suggest a direct role of the exosome in structural remodeling of the 90S pre-ribosome to drive eukaryotic ribosome synthesis. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7ajt.cif.gz | 6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7ajt.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7ajt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/7ajt ftp://data.pdbj.org/pub/pdb/validation_reports/aj/7ajt | HTTPS FTP |
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-Related structure data
Related structure data | 11807MC 7ajuC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+Protein , 19 types, 23 molecules CACBJAJBUAUCUPUQCFCGCMJFJGJHJIJJJKJNJOJPJQEKEN
+40S ribosomal protein ... , 17 types, 17 molecules DADEDFDGDHDIDJDLDNDODQDSDWDXDYDbDc
+Nucleolar complex protein ... , 2 types, 2 molecules UBUS
+U3 small nucleolar RNA-associated protein ... , 17 types, 17 molecules UDUEUFUGUHUIUJUKULUMUNUOURUTUUUVCK
+RRNA-processing protein ... , 2 types, 2 molecules UXJM
+Ribosome biogenesis protein ... , 3 types, 3 molecules UZCLJC
+Nucleolar protein ... , 2 types, 2 molecules CDCE
+Ribosomal RNA-processing protein ... , 2 types, 2 molecules CHCN
+U3 small nucleolar ribonucleoprotein protein ... , 2 types, 2 molecules CICJ
+RNA chain , 4 types, 4 molecules D2D3D4EA
+Exosome complex component ... , 9 types, 9 molecules EBECEDEEEFEGEHEIEJ
+Non-polymers , 3 types, 7 molecules
+Details
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 90S-exosome super-complex in state Pre-A1-exosome / Type: RIBOSOME / Entity ID: #1-#79 / Source: NATURAL |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 44 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software | Name: CTFFIND / Category: CTF correction |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6024 / Symmetry type: POINT |