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- PDB-7aju: Cryo-EM structure of the 90S-exosome super-complex (state Post-A1... -
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Basic information
Entry | Database: PDB / ID: 7aju | ||||||
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Title | Cryo-EM structure of the 90S-exosome super-complex (state Post-A1-exosome) | ||||||
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![]() | RIBOSOME / Ribosome biogenesis / Exosome / 90S pre-ribosome / A1 cleavage / Mtr4 | ||||||
Function / homology | ![]() 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / 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 decay by 3' to 5' exoribonuclease / nuclear polyadenylation-dependent CUT catabolic process / regulatory ncRNA 3'-end processing / box H/ACA snoRNA binding ...18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / 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 decay by 3' to 5' exoribonuclease / nuclear polyadenylation-dependent CUT catabolic process / regulatory ncRNA 3'-end processing / box H/ACA snoRNA binding / regulation of ribosomal protein gene transcription by RNA polymerase II / rRNA small subunit pseudouridine methyltransferase Nep1 / Noc4p-Nop14p complex / TRAMP-dependent tRNA surveillance pathway / RNA fragment catabolic process / rRNA 2'-O-methylation / CUT catabolic process / exosome (RNase complex) / nuclear polyadenylation-dependent rRNA catabolic process / U1 snRNA 3'-end processing / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / CURI complex / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / cytoplasmic exosome (RNase complex) / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / t-UTP complex / nuclear exosome (RNase complex) / UTP-C complex / Mpp10 complex / snoRNA guided rRNA 2'-O-methylation / Pwp2p-containing subcomplex of 90S preribosome / rRNA (pseudouridine) methyltransferase activity / rRNA modification / nuclear-transcribed mRNA catabolic process, non-stop decay / nuclear microtubule / poly(A)-dependent snoRNA 3'-end processing / regulation of rRNA processing / U4 snRNA 3'-end processing / histone H2AQ104 methyltransferase activity / : / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D sno(s)RNA binding / : / 3'-5' RNA helicase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / snRNA binding / positive regulation of RNA binding / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear mRNA surveillance / septum digestion after cytokinesis / box C/D sno(s)RNA 3'-end processing / tRNA export from nucleus / rDNA heterochromatin / rRNA catabolic process / nonfunctional rRNA decay / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methyltransferase activity / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of transcription by RNA polymerase I / positive regulation of rRNA processing / poly(A) binding / U4/U6 snRNP / single-stranded telomeric DNA binding / rRNA primary transcript binding / 90S preribosome assembly / rRNA base methylation / Negative regulators of DDX58/IFIH1 signaling / O-methyltransferase activity / SUMOylation of RNA binding proteins / sno(s)RNA-containing ribonucleoprotein complex / protein localization to nucleolus / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / U4 snRNA binding / poly(U) RNA binding / box C/D methylation guide snoRNP complex / mTORC1-mediated signalling / Protein hydroxylation / RNA catabolic process / rRNA methylation / U4 snRNP / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / U3 snoRNA binding / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / poly(A)+ mRNA export from nucleus / preribosome, small subunit precursor / establishment of cell polarity / snoRNA binding / rRNA metabolic process / positive regulation of transcription by RNA polymerase I / precatalytic spliceosome / maturation of 5.8S rRNA / Major pathway of rRNA processing in the nucleolus and cytosol / spliceosomal complex assembly / SRP-dependent cotranslational protein targeting to membrane / nucleolar large rRNA transcription by RNA polymerase I / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||
![]() | Cheng, J. / Lau, B. / Flemming, D. / Venuta, G.L. / Berninghausen, O. / Beckmann, R. / Hurt, E. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
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-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 717.4 KB | Display | |
Data in CIF | ![]() | 1.1 MB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 11808MC ![]() 7ajtC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Components
+Protein , 17 types, 20 molecules CACBUAUCUPUQCFCGCLCMJDJFJGJHJIJLJPJJEKEN
+40S ribosomal protein ... , 18 types, 18 molecules DADbDEDFDGDHDIDJDLDNDODQDSDTDWDXDYDc
+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
+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, 6 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
+Details
-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
Component | Name: 90S-exosome super-complex in state Post-A1-exosome / Type: RIBOSOME / Entity ID: #1-#75 / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: 44 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
EM software | Name: CTFFIND / Category: CTF correction |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35320 / Symmetry type: POINT |
Atomic model building | Protocol: RIGID BODY FIT |
Atomic model building | PDB-ID: 6ZQD Accession code: 6ZQD / Source name: PDB / Type: experimental model |