- EMDB-3847: Cryo-EM structure of the 90S pre-ribosome from Chaetomium thermophilum -
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Basic information
Entry
Database: EMDB / ID: EMD-3847
Title
Cryo-EM structure of the 90S pre-ribosome from Chaetomium thermophilum
Map data
Sample
The 90S Pre-ribosomne
Periodic tryptophan protein 2-like protein
Utp2
Utp3
Utp4
Utp6
Utp7
Utp10
U3 small nucleolar RNA-associated protein 11
Utp12
Utp13
Utp14
Utp15
Utp17
Utp18
Putative U3 snoRNP protein
Utp24
Utp30
Nop1
Putative nucleolar proteinNucleolus
Nop58
Snu13NHP2L1
Rrp9
RNA 3'-terminal phosphate cyclase-like protein
Bms1
Imp3
(Putative U3 small nucleolar ...) x 2
Sof1
Emg1
KRR1 small subunit processome component
Pre-rRNA-processing protein PNO1
RNA cytidine acetyltransferase
Fcf2
(40S ribosomal protein ...) x 15
Faf1
(nucleic-acidNucleic acid) x 2
ligand
Function / homology
Function and homology information
rRNA cytidine N-acetyltransferase activity / tRNA acetylation / mRNA modification / Mpp10 complex / rRNA (pseudouridine) methyltransferase activity / rRNA modification / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear microtubule / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D RNP complex ...rRNA cytidine N-acetyltransferase activity / tRNA acetylation / mRNA modification / Mpp10 complex / rRNA (pseudouridine) methyltransferase activity / rRNA modification / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear microtubule / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D RNP complex / snRNA binding / rRNA base methylation / protein localization to nucleolus / U3 snoRNA binding / rRNA export from nucleus / sno(s)RNA-containing ribonucleoprotein complex / 90S preribosome / preribosome, small subunit precursor / snoRNA binding / 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) / RNA processing / small-subunit processome / ribosomal small subunit biogenesis / nuclear periphery / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / endoribonuclease activity / catalytic activity / small ribosomal subunit rRNA binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA processing / mRNA processing / methyltransferase activity / ribosome biogenesis / cytosolic small ribosomal subunit / ribonucleoprotein complex / small ribosomal subunit / tRNA binding / methylation / rRNA binding / ribosome / structural constituent of ribosome / protein ubiquitination / translation / GTPase activity / GTP binding / nucleolus / RNA binding / ATP binding / identical protein binding / nucleus / cytoplasm
WD40/YVTN repeat-like-containing domain superfamily / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / BING4, C-terminal domain / BP28, C-terminal domain / NOP5, N-terminal / NOSIC / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / RNA 3'-terminal phosphate cyclase, insert domain / Ribosomal protein S4e, N-terminal / Ribosomal protein L23/L15e core domain superfamily ...WD40/YVTN repeat-like-containing domain superfamily / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / BING4, C-terminal domain / BP28, C-terminal domain / NOP5, N-terminal / NOSIC / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / RNA 3'-terminal phosphate cyclase, insert domain / Ribosomal protein S4e, N-terminal / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein S4e, central region / Small-subunit processome, Utp13 / U3 small nucleolar RNA-associated protein 6 / Ribosomal protein S6, eukaryotic / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / Fcf2 pre-rRNA processing, C-terminal / AARP2CN / Ribosomal protein S13/S15, N-terminal / Armadillo-type fold / Nucleolar protein 14 / Small-subunit processome, Utp14 / rRNA-processing protein Fcf1/Utp23 / Ribosome biogenesis protein BMS1/TSR1, C-terminal / Brix domain / Small-subunit processome, Utp11 / Sas10/Utp3/C1D / Small-subunit processome, Utp12 / Sof1-like protein / Nucleic acid-binding, OB-fold / Small-subunit processome, Utp21 / Helicase domain / S15/NS1, RNA-binding / Quinoprotein amine dehydrogenase, beta chain-like / Quinoprotein alcohol dehydrogenase-like superfamily / Tetratricopeptide-like helical domain superfamily / U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / 50S ribosomal protein L30e-like / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein S5/S7, eukaryotic/archaeal / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein S4/S9 / Ribosomal protein S15P / Ribosomal protein L1-like / RNA 3'-terminal phosphate cyclase domain / Ribosomal protein S7 domain / Ribosomal RNA assembly KRR1 / Periodic tryptophan protein 2 / 40S ribosomal protein S1/3, eukaryotes / U3 small nucleolar RNA-associated protein 10, N-terminal / Possible tRNA binding domain / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein S28e conserved site / Helix hairpin bin domain superfamily / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Fibrillarin, conserved site / RNA 3'-terminal phosphate cyclase type 2 / Pyrrolo-quinoline quinone beta-propeller repeat / WD40-repeat-containing domain / Ribosomal protein S4, conserved site / Ribosomal S24e conserved site / Ribosomal S11, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein S7, conserved site / Sas10 C-terminal domain / U3 small nucleolar RNA-associated protein 15, C-terminal / WD40 repeat, conserved site / Ribosomal protein S17, conserved site / G-protein beta WD-40 repeat / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein S12/S23 / Ribosomal protein S4/S9, eukaryotic/archaeal / S-adenosyl-L-methionine-dependent methyltransferase / RNA-binding S4 domain superfamily / 40S ribosomal protein S11, N-terminal / TmcA/NAT10/Kre33 / Ribosomal protein S23, eukaryotic/archaeal / RNA cytidine acetyltransferase NAT10 / Ribosomal protein S8 superfamily / Nop domain superfamily / WD40-repeat-containing domain superfamily / RNA 3'-terminal phosphate cyclase, insert domain superfamily / K Homology domain, type 1 superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S11 superfamily / RNA 3'-terminal phosphate cyclase domain superfamily / Bms1/Tsr1-type G domain / Ribosome biogenesis protein Bms1, N-terminal / Ribosomal protein S4e, central domain superfamily / Ribosomal RNA-processing protein Rrp9-like / Ribosome biogenesis protein Bms1/Tsr1 / Fcf2/DNTTIP2 / Pre-rRNA-processing protein PNO1-like
Putative U3 small nucleolar ribonucleoprotein protein / 40S ribosomal protein S28-like protein / Uncharacterized protein / WD_REPEATS_REGION domain-containing protein / 40S ribosomal protein S16-like protein / WD_REPEATS_REGION domain-containing protein / WD_REPEATS_REGION domain-containing protein / S4 RNA-binding domain-containing protein / Uncharacterized protein / PINc domain-containing protein ...Putative U3 small nucleolar ribonucleoprotein protein / 40S ribosomal protein S28-like protein / Uncharacterized protein / WD_REPEATS_REGION domain-containing protein / 40S ribosomal protein S16-like protein / WD_REPEATS_REGION domain-containing protein / WD_REPEATS_REGION domain-containing protein / S4 RNA-binding domain-containing protein / Uncharacterized protein / PINc domain-containing protein / WD_REPEATS_REGION domain-containing protein / Putative U3 small nucleolar ribonucleoprotein / 40S ribosomal protein S11-like protein / U3 small nucleolar RNA-associated protein 11 / Periodic tryptophan protein 2-like protein / 40S ribosomal protein S14-like protein / Uncharacterized protein / WD_REPEATS_REGION domain-containing protein / Ribonucloprotein / Histone-glutamine methyltransferase / 40S ribosomal protein S22-like protein / 40S ribosomal protein S7 / Uncharacterized protein / 40S ribosomal protein s5-like protein / Putative U3 snoRNP protein / 40S ribosomal protein S4 / 40S ribosomal protein s23-like protein / 40S ribosomal protein S6 / 40S ribosomal protein S8 / DDB1- and CUL4-associated factor 13 / Nucleolar protein 58 / WD_REPEATS_REGION domain-containing protein / WD_REPEATS_REGION domain-containing protein / 40S ribosomal protein S13-like protein / RNA 3'-terminal phosphate cyclase-like protein / 40S ribosomal protein s9-like protein / RNA cytidine acetyltransferase / Uncharacterized protein / Nucleolar protein 58 / Uncharacterized protein / Pre-rRNA-processing protein PNO1 / KRR1 small subunit processome component / Bms1-type G domain-containing protein / Fcf2 domain-containing protein / Sas10 domain-containing protein / Uncharacterized protein / U3 small nucleolar RNA-associated protein 10 / 40S ribosomal protein S1 / 40S ribosomal protein S24
Journal: Nat Struct Mol Biol / Year: 2017 Title: 3.2-Å-resolution structure of the 90S preribosome before A1 pre-rRNA cleavage. Authors: Jingdong Cheng / Nikola Kellner / Otto Berninghausen / Ed Hurt / Roland Beckmann / Abstract: The 40S small ribosomal subunit is cotranscriptionally assembled in the nucleolus as part of a large chaperone complex called the 90S preribosome or small-subunit processome. Here, we present the 3.2- ...The 40S small ribosomal subunit is cotranscriptionally assembled in the nucleolus as part of a large chaperone complex called the 90S preribosome or small-subunit processome. Here, we present the 3.2-Å-resolution structure of the Chaetomium thermophilum 90S preribosome, which allowed us to build atomic structures for 34 assembly factors, including the Mpp10 complex, Bms1, Utp14 and Utp18, and the complete U3 small nucleolar ribonucleoprotein. Moreover, we visualized the U3 RNA heteroduplexes with a 5' external transcribed spacer (5' ETS) and pre-18S RNA, and their stabilization by 90S factors. Overall, the structure explains how a highly intertwined network of assembly factors and pre-rRNA guide the sequential, independent folding of the individual pre-40S domains while the RNA regions forming the 40S active sites are kept immature. Finally, by identifying the unprocessed A1 cleavage site and the nearby Utp24 endonuclease, we suggest a proofreading model for regulated 5'-ETS separation and 90S-pre-40S transition.
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