- PDB-6rxt: Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaet... -
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Entry
Database: PDB / ID: 6rxt
Title
Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state A
Components
(40S ribosomal protein ...) x 10
(Putative U3 small nucleolar ...) x 2
35S ribosomal RNA
Bms1
Emg1
Enp1
Faf1
Fcf2
Imp3
KRR1 small subunit processome component
Kre33
Noc4
Nop1
Nop58
Periodic tryptophan protein 2-like protein
Pre-rRNA-processing protein PNO1
Putative U3 snoRNP protein
Putative nucleolar proteinNucleolus
Putative ribosomal protein
RNA 3'-terminal phosphate cyclase-like protein
Rrp9
Sof1
U3 small nucleolar RNA-associated protein 11
U3 snoRNA
UTP10
Utp12
Utp13"
Utp14
Utp15
Utp16
Utp17
Utp18
Utp2
Utp24
Utp30
Utp3
Utp4
Utp5"
Utp6
Utp7
Utp8
snu13NHP2L1
Keywords
RIBOSOME / ribosome biogenesis / rRNA
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 / catalytic activity / small ribosomal subunit rRNA binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA processing / ribosome biogenesis / mRNA processing / methyltransferase activity / 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 / membrane / ATP binding / identical protein binding / nucleus / cytoplasm
Ribosomal protein L1p/L10e family / TmcA/NAT10/Kre33 / 40S ribosomal protein S1/3, eukaryotes / Possible tRNA binding domain / 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 / S-adenosyl-L-methionine-dependent methyltransferase ...Ribosomal protein L1p/L10e family / TmcA/NAT10/Kre33 / 40S ribosomal protein S1/3, eukaryotes / Possible tRNA binding domain / 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 / S-adenosyl-L-methionine-dependent methyltransferase / 50S ribosomal protein L30e-like / Bms1/Tsr1-type G domain / RNA cytidine acetyltransferase NAT10 / P-loop containing nucleoside triphosphate hydrolase / 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-binding S4 domain superfamily / RNA 3'-terminal phosphate cyclase domain superfamily / Ribosome biogenesis protein Bms1, N-terminal / Ribosomal RNA-processing protein Rrp9-like / 30s ribosomal protein S13, C-terminal / Nucleolar complex protein 4 / Fcf2/DNTTIP2 / U3 small nucleolar RNA-associated protein 15, C-terminal / Ribosomal protein L1, 3-layer alpha/beta-sandwich / RNA 3'-terminal phosphate cyclase type 2 / WD40-repeat-containing domain / Ribosomal protein S4, conserved site / Ribosomal S11, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S3Ae, conserved site / Pyrrolo-quinoline quinone beta-propeller repeat / Ribosomal protein L7Ae/L8/Nhp2 family / Sas10 C-terminal domain / WD40 repeat, conserved site / Periodic tryptophan protein 2 / G-protein beta WD-40 repeat / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein S7, conserved site / Fibrillarin, conserved site / U3 small nucleolar RNA-associated protein 10, N-terminal / Ribosomal protein S4/S9 / Ribosomal protein S15P / Ribosomal protein L1-like / RNA 3'-terminal phosphate cyclase domain / Ribosomal RNA assembly KRR1 / Ribosome biogenesis protein Bms1/Tsr1 / Pre-rRNA-processing protein PNO1-like / WD40/YVTN repeat-like-containing domain superfamily / Sas10/Utp3/C1D family / Ribosomal protein S15 / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S11 / Ribosomal protein S9/S16 / Ribosomal protein S13/S18 / Ribosomal protein S8 / Ribosomal protein S12/S23 / Ribosomal protein S28e / Dip2/Utp12 Family / Nop14-like family / Sas10 C-terminal domain / Ribosomal protein S7p/S5e / U3 small nucleolar RNA-associated protein 6 / BING4CT (NUC141) domain / BP28CT (NUC211) domain / U3 small nucleolar RNA-associated protein 10 / Utp11 protein / Utp13 specific WD40 associated domain / Utp14 protein / UTP15 C terminal / U3 snoRNA associated / CBF/Mak21 family / Utp21 specific WD40 associated putative domain / Ribosomal protein S7e / Ribosomal S3Ae family / U3 small nucleolar RNA-associated protein 10 / AARP2CN (NUC121) domain / WD repeat-containing protein WDR46/Utp7 / Krr1, KH1 domain / Nop, C-terminal domain / Fibrillarin / snoRNA binding domain, fibrillarin / NOP5NT (NUC127) domain / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / WD domain, G-beta repeat / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase (RTC), insert domain / 40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal / Ribosomal protein S4/S9 N-terminal domain / Bystin / S4 domain / Brix domain / Mpp10 protein / Sof1-like domain
40S ribosomal protein s5-like protein / 40S ribosomal protein s9-like protein / RNA 3'-terminal phosphate cyclase-like protein / 40S ribosomal protein s23-like protein / DDB1- and CUL4-associated factor 13 / RNA cytidine acetyltransferase / 40S ribosomal protein S13-like protein / WD_REPEATS_REGION domain-containing protein / Nucleolar protein 58 / WD_REPEATS_REGION domain-containing protein ...40S ribosomal protein s5-like protein / 40S ribosomal protein s9-like protein / RNA 3'-terminal phosphate cyclase-like protein / 40S ribosomal protein s23-like protein / DDB1- and CUL4-associated factor 13 / RNA cytidine acetyltransferase / 40S ribosomal protein S13-like protein / WD_REPEATS_REGION domain-containing protein / Nucleolar protein 58 / WD_REPEATS_REGION domain-containing protein / Utp12 domain-containing protein / CBF domain-containing protein / Putative ribosomal protein / Uncharacterized protein / Nucleolar protein 58 / WD_REPEATS_REGION domain-containing protein / Putative U3 small nucleolar ribonucleoprotein / Uncharacterized protein / S4 RNA-binding domain-containing protein / WD_REPEATS_REGION domain-containing protein / WD_REPEATS_REGION domain-containing protein / 40S ribosomal protein S16-like protein / Uncharacterized protein / U3 small nucleolar RNA-associated protein 11 / 40S ribosomal protein S28-like protein / Putative U3 small nucleolar ribonucleoprotein protein / Uncharacterized protein / 40S ribosomal protein S7 / Putative U3 snoRNP protein / Uncharacterized protein / WD_REPEATS_REGION domain-containing protein / Periodic tryptophan protein 2-like protein / 40S ribosomal protein S1 / U3 small nucleolar RNA-associated protein 10 / Pre-rRNA-processing protein PNO1 / KRR1 small subunit processome component / Bms1-type G domain-containing protein / Fcf2 domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / 40S ribosomal protein S14-like protein / Uncharacterized protein CTHT_0071780 / 40S ribosomal protein S22-like protein / Histone-glutamine methyltransferase / Ribonucloprotein / WD_REPEATS_REGION domain-containing protein / Uncharacterized protein / Sas10 domain-containing protein
Biological species
Chaetomium thermophilum (fungus)
Method
ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7 Å
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 ...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.
Protein , 38 types, 43 molecules UAUBUCUDUFUGUJUKULUMUNUOUQURUUUXUZCACBCCCDCECFCGCHCICJCMCNCO...
#1: Protein
Periodictryptophanprotein2-likeprotein
Mass: 100817.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SF93
#2: Protein
Utp2
Mass: 103960.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SDW0
#3: Protein
Utp3 /
Mass: 73214.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S4H3
#4: Protein
Utp4
Mass: 97696.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SCT7
#5: Protein
Utp6 /
Mass: 46924.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S387
#6: Protein
Utp7
Mass: 63629.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0RZ99
#7: Protein
UTP10
Mass: 198508.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S5L1
#8: Protein
U3smallnucleolarRNA-associatedprotein11 / U3 snoRNA-associated protein 11
Mass: 31379.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SF32
#9: Protein
Utp12
Mass: 107573.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0RZL9
#10: Protein
Utp13"
Mass: 100430.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SG95
#11: Protein
Utp14
Mass: 104741.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S8Y4
#12: Protein
Utp15 /
Mass: 60524.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SEI5
#13: Protein
Utp17
Mass: 105039.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SCS8
#14: Protein
Utp18 /
Mass: 69055.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SBN9
#15: Protein
PutativeU3snoRNPprotein
Mass: 115122.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S872
#16: Protein
Utp24
Mass: 22135.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus)
#17: Protein
Utp30
Mass: 43700.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S7X0
#18: Protein
Nop1
Mass: 32960.844 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SGY2
#19: Protein
Putativenucleolarprotein / Nucleolus
Mass: 57830.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S2U4
#20: Protein
Nop58 /
Mass: 64292.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0RYF6
#21: Protein
snu13 / NHP2L1
Mass: 13831.854 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SGM0
#22: Protein
Rrp9 /
Mass: 69610.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SG51
#23: Protein
RNA3'-terminalphosphatecyclase-likeprotein
Mass: 43399.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S0B1
#24: Protein
Bms1
Mass: 134172.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S445
#25: Protein
Imp3 /
Mass: 21802.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SDL4
#28: Protein
Sof1
Mass: 50869.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0RY94
#29: Protein
Emg1 /
Mass: 27936.164 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SAY9
#30: Protein
KRR1smallsubunitprocessomecomponent / / KRR-R motif-containing protein 1
Mass: 37500.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S3V7
#31: Protein
Pre-rRNA-processingproteinPNO1
Mass: 28715.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S3T2
#32: Protein
Kre33
Mass: 119795.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) References: UniProt: G0S273, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#33: Protein
Fcf2
Mass: 22569.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S4E3
#44: Protein
Faf1 /
Mass: 34576.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S5F1
#47: Protein
Utp8
Mass: 102421.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: P0CT47
#48: Protein
Utp5"
Mass: 44663.355 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0RYX2
#49: Protein
Noc4
Mass: 63331.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0RZL4
#50: Protein
Putativeribosomalprotein /
Mass: 17826.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S6J7
#51: Protein
Enp1
Mass: 54319.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S5J4
#52: Protein
Utp16
Mass: 40726.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S612
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