EMDB-10054: Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaet...

Basic information

• Entry: Database: EMDB / ID: EMD-10054
• Title: Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state C

Sample

• Complex: 90S pre-ribosome, state C
  • Protein or peptide: x 61 types
  • RNA: x 2 types
• Ligand: x 1 types

• Keywords: ribosome / ribosome biogenesis / rRNA

Function / homology

Function:

rRNA acetylation involved in maturation of SSU-rRNA / rRNA cytidine N-acetyltransferase activity / tRNA N-acetyltransferase activity / tRNA acetylation / Noc4p-Nop14p complex / tRNA wobble cytosine modification / CURI complex / t-UTP complex / UTP-C complex / Mpp10 complex / Pwp2p-containing subcomplex of 90S preribosome / rRNA (pseudouridine) methyltransferase activity / 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 / tRNA export from nucleus / 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) / positive regulation of rRNA processing / rRNA primary transcript binding / rRNA base methylation / sno(s)RNA-containing ribonucleoprotein complex / box C/D methylation guide snoRNP complex / U3 snoRNA binding / preribosome, small subunit precursor / snoRNA binding / positive regulation of transcription by RNA polymerase I / precatalytic spliceosome / RNA processing / Cajal body / U4/U6 x U5 tri-snRNP complex / 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) / maturation of LSU-rRNA / methyltransferase activity / maturation of SSU-rRNA / small-subunit processome / mRNA splicing, via spliceosome / rRNA processing / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / methylation / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / GTPase activity / mRNA binding / nucleolus / regulation of transcription by RNA polymerase II / GTP binding / RNA binding / ATP binding / nucleus / cytoplasm / cytosol

Domain/homology:

Apoptosis-antagonizing transcription factor, C-terminal / AATF leucine zipper-containing domain / Protein AATF/Bfr2 / Apoptosis-antagonizing transcription factor, C-terminal / Apoptosis antagonizing transcription factor / NUC153 / Nucleolar protein 10/Enp2 / NUC153 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 / U3 small nucleolar RNA-associated protein 20, N-terminal / U3 snoRNA associated / Nucleolar complex protein 4 / U3 small nucleolar RNA-associated protein 20, C-terminal / U3 small nucleolar RNA-associated protein 20, N-terminal / U3 snoRNA associated / U3 small nucleolar RNA-associated protein 20, C-terminal / Nucleolar protein 14 / Nop14-like family / U3 small nucleolar RNA-associated protein 6 / U3 small nucleolar RNA-associated protein 6 / NOL6/Upt22 / Small-subunit processome, Utp11 / Sof1-like protein / BING4, C-terminal domain / Fcf2 pre-rRNA processing, C-terminal / Nrap protein domain 1 / Nrap protein, domain 2 / Nrap protein, domain 3 / Nrap protein, domain 4 / Nrap protein, domain 5 / Nrap protein, domain 6 / Fcf2/DNTTIP2 / WD repeat-containing protein WDR46/Utp7 / Nrap protein domain 1 / Utp11 protein / Sof1-like domain / BING4CT (NUC141) domain / Fcf2 pre-rRNA processing / Nrap protein PAP/OAS-like domain / Nrap protein domain 3 / Nrap protein nucleotidyltransferase domain 4 / Nrap protein PAP/OAS1-like domain 5 / Nrap protein domain 6 / BING4CT (NUC141) domain / Ribosomal RNA-processing protein 7, C-terminal domain / Ribosomal RNA-processing protein 7 / Rrp7, RRM-like N-terminal domain / Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain / Rrp7 RRM-like N-terminal domain / Small-subunit processome, Utp14 / U3 small nucleolar RNA-associated protein 15, C-terminal / Utp14 protein / UTP15 C terminal / Sas10 C-terminal domain / Sas10 C-terminal domain / Nucleolar protein 58/56, N-terminal / U3 small nucleolar RNA-associated protein 18 / NOP5NT (NUC127) domain / BP28, C-terminal domain / 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 / BP28CT (NUC211) domain / U3 small nucleolar RNA-associated protein 13, C-terminal / Periodic tryptophan protein 2 / Utp13 specific WD40 associated domain / Small-subunit processome, Utp12 / Ribosomal RNA-processing protein Rrp9-like / Dip2/Utp12 Family / Sas10/Utp3/C1D / Small-subunit processome, Utp21 / U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / RNA 3'-terminal phosphate cyclase type 2 / Sas10/Utp3/C1D family / Mpp10 protein / 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

Component:

40S ribosomal protein s23-like protein / 40S ribosomal protein S6 / 40S ribosomal protein S8 / DDB1- and CUL4-associated factor 13 / Nucleolar protein 58 / Small-subunit processome Utp12 domain-containing protein / BING4 C-terminal domain-containing protein / CCAAT-binding factor domain-containing protein / Small-subunit processome Utp12 domain-containing protein / 40S ribosomal protein S13-like protein / RNA 3'-terminal phosphate cyclase-like protein / 40S ribosomal protein s9-like protein / 40S ribosomal protein S4 / Ribosomal protein s27-like protein / 40S ribosomal protein s5-like protein / RNA cytidine acetyltransferase / U3 small nucleolar RNA-associated protein 22 / Nucleolar protein 56 / U3 snoRNP protein / Pre-rRNA-processing protein PNO1 / KRR1 small subunit processome component / Bms1-type G domain-containing protein / Fcf2 pre-rRNA processing C-terminal domain-containing protein / Sas10 C-terminal domain-containing protein / Uncharacterized protein / Bystin-like protein / U3 small nucleolar RNA-associated protein 10 / Uncharacterized protein / Putative ribosomal protein / Small ribosomal subunit protein eS1 / Putative U3 snoRNP protein / 40S ribosomal protein S7 / Uncharacterized protein / Ribosome biogenesis protein ENP2 / Putative U3 small nucleolar ribonucleoprotein protein / 40S ribosomal protein S28-like protein / Protein BFR2 / Nucleolar essential protein 1 / Uncharacterized protein / 40S ribosomal protein S16-like protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Nucleolar complex protein 14 / U3 small nucleolar ribonucleoprotein protein IMP4 / U3 small nucleolar RNA-associated protein 15 C-terminal domain-containing protein / 40S ribosomal protein S11-like protein / U3 small nucleolar RNA-associated protein 11 / Periodic tryptophan protein 2-like protein / 40S ribosomal protein S19-like protein / 40S ribosomal protein S14-like protein / Ribosomal RNA-processing protein / U3 small nucleolar RNA-associated protein 13 C-terminal domain-containing protein / 13 kDa ribonucleoprotein-associated protein / rRNA 2'-O-methyltransferase fibrillarin / 40S ribosomal protein S22-like protein / Uncharacterized protein / Uncharacterized protein CTHT_0071780 / Small ribosomal subunit protein eS24

• Biological species: Chaetomium thermophilum (fungus)
• Method: single particle reconstruction / cryo EM / Resolution: 7.1 Å
• Authors: Cheng J / Kellner N
• Citation: Journal: Mol Cell / Year: 2019; Title: Thermophile 90S Pre-ribosome Structures Reveal the Reverse Order of Co-transcriptional 18S rRNA Subdomain Integration.; Authors: Jingdong Cheng / Jochen Baßler / Paulina Fischer / Benjamin Lau / Nikola Kellner / Ruth Kunze / Sabine Griesel / Martina Kallas / Otto Berninghausen / Daniela Strauss / Roland Beckmann / Ed Hurt / ; Abstract: Eukaryotic ribosome biogenesis involves RNA folding and processing that depend on assembly factors and small nucleolar RNAs (snoRNAs). The 90S (SSU-processome) is the earliest pre-ribosome structurally analyzed, which was suggested to assemble stepwise along the growing pre-rRNA from 5' > 3', but this directionality may not be accurate. Here, by analyzing the structure of a series of 90S assembly intermediates from Chaetomium thermophilum, we discover a reverse order of 18S rRNA subdomain incorporation. Large parts of the 18S rRNA 3' and central domains assemble first into the 90S before the 5' domain is integrated. This final incorporation depends on a contact between a heterotrimer Enp2-Bfr2-Lcp5 recruited to the flexible 5' domain and Kre33, which reconstitutes the Kre33-Enp-Brf2-Lcp5 module on the compacted 90S. Keeping the 5' domain temporarily segregated from the 90S scaffold could provide extra time to complete the multifaceted 5' domain folding, which depends on a distinct set of snoRNAs and processing factors.

History

Deposition	Jun 10, 2019	-
Header (metadata) release	Aug 14, 2019	-
Map release	Aug 14, 2019	-
Update	May 22, 2024	-
Current status	May 22, 2024	Processing site: PDBe / Status: Released