rRNA acetylation involved in maturation of SSU-rRNA / rRNA cytidine N-acetyltransferase activity / tRNA N-acetyltransferase activity / tRNA acetylation / rRNA small subunit pseudouridine methyltransferase Nep1 / tRNA wobble cytosine modification / t-UTP complex / Mpp10 complex / Pwp2p-containing subcomplex of 90S preribosome / rRNA (pseudouridine) methyltransferase activity ...rRNA acetylation involved in maturation of SSU-rRNA / rRNA cytidine N-acetyltransferase activity / tRNA N-acetyltransferase activity / tRNA acetylation / rRNA small subunit pseudouridine methyltransferase Nep1 / tRNA wobble cytosine modification / t-UTP complex / Mpp10 complex / Pwp2p-containing subcomplex of 90S preribosome / rRNA (pseudouridine) methyltransferase activity / nuclear microtubule / regulation of rRNA processing / histone H2AQ104 methyltransferase activity / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D sno(s)RNA 3'-end processing / 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) / rRNA primary transcript binding / ribonuclease P activity / rRNA base methylation / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / rRNA methylation / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / tRNA processing / U3 snoRNA binding / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / snoRNA binding / positive regulation of transcription by RNA polymerase I / 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 / 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) / L13a-mediated translational silencing of Ceruloplasmin expression / regulation of translational fidelity / RNA nuclease activity / 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) / enzyme activator activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / RNA endonuclease activity / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear periphery / Transferases; Transferring one-carbon groups; Methyltransferases / maturation of LSU-rRNA / maturation of SSU-rRNA / small-subunit processome / rRNA processing / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / GTPase activity / mRNA binding / nucleolus / GTP binding / ATP hydrolysis activity / mitochondrion / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function
: / : / Archaeal Nop5/56-rel, N-terminal domain / Possible tRNA binding domain / RNA cytidine acetyltransferase NAT10 / Possible tRNA binding domain / Helicase domain / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / TmcA/NAT10/Kre33 / : ...: / : / Archaeal Nop5/56-rel, N-terminal domain / Possible tRNA binding domain / RNA cytidine acetyltransferase NAT10 / Possible tRNA binding domain / Helicase domain / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / TmcA/NAT10/Kre33 / : / : / : / Helicase / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / GNAT acetyltransferase 2 / KRR1 small subunit processome component, second KH domain / Ribosomal RNA assembly KRR1 / rRNA-processing protein Fcf1, PIN domain / rRNA-processing protein Fcf1/Utp23 / Fcf1 / BP28, C-terminal domain / RNA 3'-terminal phosphate cyclase-like, conserved site / U3 small nucleolar RNA-associated protein 10, N-terminal / Ribosome biogenesis protein Bms1, N-terminal / U3 small nucleolar RNA-associated protein 10 / BP28CT (NUC211) domain / U3 small nucleolar RNA-associated protein 10 / RNA 3'-terminal phosphate cyclase signature. / BP28CT (NUC211) domain / Ribosomal RNA-processing protein Rrp9-like / Small-subunit processome, Utp21 / RNA 3'-terminal phosphate cyclase type 2 / Utp21 specific WD40 associated putative domain / Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / EMG1/NEP1 methyltransferase / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase domain / RNA 3'-terminal phosphate cyclase, insert domain superfamily / RNA 3'-terminal phosphate cyclase domain superfamily / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase (RTC), insert domain / Nucleolar protein Nop56/Nop58 / Krr1, KH1 domain / Krr1 KH1 domain / rRNA 2'-O-methyltransferase fibrillarin-like / Fibrillarin, conserved site / Fibrillarin / Fibrillarin signature. / Fibrillarin / U3 snoRNP protein/Ribosome production factor 1 / Large family of predicted nucleotide-binding domains / Ribosome biogenesis protein BMS1/TSR1, C-terminal / AARP2CN / Bms1/Tsr1-type G domain / Ribosome biogenesis protein Bms1/Tsr1 / 40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal / AARP2CN (NUC121) domain / Bms1-type guanine nucleotide-binding (G) domain profile. / AARP2CN (NUC121) domain / Protein of unknown function (DUF663) / PIN domain / Ribosomal protein L7Ae, archaea / NOSIC / NOSIC (NUC001) domain / Nop domain / Nop domain superfamily / Nop, C-terminal domain / snoRNA binding domain, fibrillarin / Nop domain profile. / Anaphase-promoting complex subunit 4, WD40 domain / Brix domain / Brix domain / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Brix domain profile. / Brix / Anaphase-promoting complex subunit 4 WD40 domain / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / K Homology domain, type 1 superfamily / PIN-like domain superfamily / Quinoprotein alcohol dehydrogenase-like superfamily / GNAT domain / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S7e / Ribosomal protein S7e / Ribosomal protein L1, 3-layer alpha/beta-sandwich Similarity search - Domain/homology
C/D box methylation guide ribonucleoprotein complex aNOP56 subunit / 40S ribosomal protein S6 / RNA cytidine acetyltransferase / KRR1 small subunit processome component / U3 small nucleolar RNA-associated protein 10 / Uncharacterized protein / Uncharacterized protein / PIN domain-containing protein / U3 small nucleolar ribonucleoprotein protein IMP4 / 40S ribosomal protein S24 ...C/D box methylation guide ribonucleoprotein complex aNOP56 subunit / 40S ribosomal protein S6 / RNA cytidine acetyltransferase / KRR1 small subunit processome component / U3 small nucleolar RNA-associated protein 10 / Uncharacterized protein / Uncharacterized protein / PIN domain-containing protein / U3 small nucleolar ribonucleoprotein protein IMP4 / 40S ribosomal protein S24 / 40S ribosomal protein S7 / Small ribosomal subunit protein uS4A / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS11A / Small ribosomal subunit protein uS8A / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein uS9A / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein eL8 / Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase / U3 small nucleolar RNA-associated protein 21 / Ribosomal RNA small subunit methyltransferase NEP1 / Ribosomal RNA-processing protein 9 / RNA 3'-terminal phosphate cyclase-like protein / Ribosome biogenesis protein BMS1 / 40S ribosomal protein S8 / 40S ribosomal protein S11, putative / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS28A Similarity search - Component
Biological species
Chaetomium thermophilum (fungus)
Method
single particle reconstruction / cryo EM / Resolution: 7.3 Å
Journal: Cell / Year: 2016 Title: Architecture of the 90S Pre-ribosome: A Structural View on the Birth of the Eukaryotic Ribosome. Authors: Markus Kornprobst / Martin Turk / Nikola Kellner / Jingdong Cheng / Dirk Flemming / Isabelle Koš-Braun / Martin Koš / Matthias Thoms / Otto Berninghausen / Roland Beckmann / Ed Hurt / Abstract: The 90S pre-ribosome is an early biogenesis intermediate formed during co-transcriptional ribosome formation, composed of ∼70 assembly factors and several small nucleolar RNAs (snoRNAs) that ...The 90S pre-ribosome is an early biogenesis intermediate formed during co-transcriptional ribosome formation, composed of ∼70 assembly factors and several small nucleolar RNAs (snoRNAs) that associate with nascent pre-rRNA. We report the cryo-EM structure of the Chaetomium thermophilum 90S pre-ribosome, revealing how a network of biogenesis factors including 19 β-propellers and large α-solenoid proteins engulfs the pre-rRNA. Within the 90S pre-ribosome, we identify the UTP-A, UTP-B, Mpp10-Imp3-Imp4, Bms1-Rcl1, and U3 snoRNP modules, which are organized around 5'-ETS and partially folded 18S rRNA. The U3 snoRNP is strategically positioned at the center of the 90S particle to perform its multiple tasks during pre-rRNA folding and processing. The architecture of the elusive 90S pre-ribosome gives unprecedented structural insight into the early steps of pre-rRNA maturation. Nascent rRNA that is co-transcriptionally folded and given a particular shape by encapsulation within a dedicated mold-like structure is reminiscent of how polypeptides use chaperone chambers for their protein folding.
History
Deposition
Apr 5, 2016
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Header (metadata) release
Aug 3, 2016
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Map release
Aug 3, 2016
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Update
Aug 3, 2016
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Current status
Aug 3, 2016
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
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