- PDB-6rxy: Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaet... -
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Entry
Database: PDB / ID: 6rxy
Title
Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state a
Components
(40S ribosomal protein ...) x 9
(U3 small nucleolar RNA-associated protein ...) x 2
35S rRNA
Bms1
Emg1
Enp1
Faf1
Fcf2
Imp3
Imp4
KRR1 small subunit processome component
Kre33
Mpp10
Noc4
Nop1
Nop56
Nop58
Periodic tryptophan protein 2-like protein
Pre-rRNA-processing protein PNO1
RNA 3'-terminal phosphate cyclase-like protein
Rps1840S ribosomal protein S18
Rrp5
Rrp7
Rrp9
Snu13NHP2L1
Sof1
U3 snoRNA
Utp10
Utp12
Utp13
Utp14
Utp15
Utp16
Utp17
Utp18
Utp2
Utp21
Utp24
Utp30
Utp3
Utp4
Utp5
Utp6
Utp7
Utp8
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 / RNA splicing / small ribosomal subunit rRNA binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA processing / mRNA processing / ribosome biogenesis / methyltransferase activity / cytosolic small ribosomal subunit / ribonucleoprotein complex / small ribosomal subunit / tRNA binding / nucleic acid 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 / WD40-repeat-containing domain superfamily / 50S ribosomal protein L30e-like / Bms1/Tsr1-type G domain / TmcA/NAT10/Kre33 / RNA cytidine acetyltransferase NAT10 / Nrap protein domain 1 / Nrap protein, domain 2 / Nrap protein, domain 3 / Nrap protein, domain 4 ...Ribosomal protein L1p/L10e family / WD40-repeat-containing domain superfamily / 50S ribosomal protein L30e-like / Bms1/Tsr1-type G domain / TmcA/NAT10/Kre33 / RNA cytidine acetyltransferase NAT10 / Nrap protein domain 1 / Nrap protein, domain 2 / Nrap protein, domain 3 / Nrap protein, domain 4 / Nrap protein, domain 5 / Nrap protein, domain 6 / Ribosomal protein S8 superfamily / Nop domain superfamily / RNA 3'-terminal phosphate cyclase, insert domain superfamily / Alpha/beta knot methyltransferases / 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 / Ribosome biogenesis protein Bms1/Tsr1 / Fcf2/DNTTIP2 / Pre-rRNA-processing protein PNO1-like / U3 small nucleolar RNA-associated protein 10 / WD repeat-containing protein WDR46/Utp7 / S-adenosyl-L-methionine-dependent methyltransferase / tRNA (guanine-N1-)-methyltransferase, N-terminal / Rrp7, RRM-like N-terminal domain / Ribosomal protein S4/S9 / Pyrrolo-quinoline quinone beta-propeller repeat / Ribosomal protein L7Ae/L8/Nhp2 family / Sas10 C-terminal domain / U3 small nucleolar RNA-associated protein 15, C-terminal / Tetratricopeptide repeat / WD40 repeat, conserved site / 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 / RNA-binding domain, S1 / Helix hairpin bin domain superfamily / Ribosomal protein S15P / Ribosomal protein L1-like / RNA 3'-terminal phosphate cyclase domain / Ribosomal protein S7 domain / Ribosomal RNA assembly KRR1 / Ribosomal RNA-processing protein 7, C-terminal domain / Periodic tryptophan protein 2 / Nucleolar complex protein 4 / P-loop containing nucleoside triphosphate hydrolase / Possible tRNA binding domain / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein S28e conserved site / Ribosomal RNA-processing protein 7 / Krr1, KH1 domain / Ribosomal S11, conserved site / U3 small nucleolar RNA-associated protein 10 / Ribosomal protein S13/S18 / Ribosomal protein S8 / Ribosomal protein S12/S23 / Ribosomal protein S28e / S1 RNA binding domain / Dip2/Utp12 Family / Nop14-like family / Sas10/Utp3/C1D family / Sas10 C-terminal domain / U3 small nucleolar RNA-associated protein 6 / BING4CT (NUC141) domain / BP28CT (NUC211) domain / Utp11 protein / Ribosomal protein S11 / Utp13 specific WD40 associated domain / Utp14 protein / UTP15 C terminal / U3 snoRNA associated / CBF/Mak21 family / Utp21 specific WD40 associated putative domain / Nrap protein domain 1 / 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 / Ribosomal protein S9/S16 / Ribosomal S13/S15 N-terminal domain / Nop, C-terminal domain / Brix domain / Nucleotidyltransferase superfamily / 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
WD_REPEATS_REGION domain-containing protein / CBF domain-containing protein / RNA cytidine acetyltransferase / 40S ribosomal protein S13-like protein / Nucleolar protein 58 / WD_REPEATS_REGION domain-containing protein / RNA 3'-terminal phosphate cyclase-like protein / Utp12 domain-containing protein / DDB1- and CUL4-associated factor 13 / 40S ribosomal protein s23-like protein ...WD_REPEATS_REGION domain-containing protein / CBF domain-containing protein / RNA cytidine acetyltransferase / 40S ribosomal protein S13-like protein / Nucleolar protein 58 / WD_REPEATS_REGION domain-containing protein / RNA 3'-terminal phosphate cyclase-like protein / Utp12 domain-containing protein / DDB1- and CUL4-associated factor 13 / 40S ribosomal protein s23-like protein / 40S ribosomal protein s9-like protein / 40S ribosomal protein s5-like protein / Uncharacterized protein / Uncharacterized protein / U3 small nucleolar RNA-associated protein 22 / Uncharacterized protein / Uncharacterized protein / 40S ribosomal protein S14-like protein / Periodic tryptophan protein 2-like protein / U3 small nucleolar RNA-associated protein 11 / WD_REPEATS_REGION domain-containing protein / Putative U3 small nucleolar ribonucleoprotein / S4 RNA-binding domain-containing protein / Ribonucloprotein / Uncharacterized protein / WD_REPEATS_REGION domain-containing protein / WD_REPEATS_REGION domain-containing protein / 40S ribosomal protein S16-like protein / WD_REPEATS_REGION domain-containing protein / Uncharacterized protein / 40S ribosomal protein S28-like protein / WD_REPEATS_REGION domain-containing protein / Histone-glutamine methyltransferase / Nucleolar protein 58 / Uncharacterized protein / Putative U3 small nucleolar ribonucleoprotein 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 / 40S ribosomal protein S22-like protein / Uncharacterized protein / Putative ribosomal protein / Uncharacterized protein / Uncharacterized protein / Putative U3 snoRNP protein / 40S ribosomal protein S7 / Uncharacterized protein CTHT_0071780 / U3 small nucleolar RNA-associated protein 10
Biological species
Chaetomium thermophilum (fungus)
Method
ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 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 , 41 types, 46 molecules UAUBUCUDUFUGUJULUMUNUOUQURUUUXUZCACBCCCDCECFCGCHCICJCKCLCMCN...
#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
#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
Utp21
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
Nop56
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
#26: Protein
Imp4 /
Mass: 34216.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SE90
#27: Protein
Mpp10
Mass: 86082.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S9I7
#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
#43: 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
Rrp7
Mass: 36366.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SDB8
#48: 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
#49: 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
#50: 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
#51: Protein
Rps18 / 40S ribosomal protein S18
Mass: 17826.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S6J7
#52: 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
#53: 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
#54: Protein
Rrp5
Mass: 197449.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S6T5
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U3 small nucleolar RNA-associated protein ... , 2 types, 2 molecules UKUV
#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
#46: Protein
U3smallnucleolarRNA-associatedprotein22
Mass: 131105.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S2E0
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40S ribosomal protein ... , 9 types, 9 molecules CcCeCgChCiCjCmCnCp
#34: Protein
40Sribosomalproteins5-likeprotein / Ribosome
Mass: 23679.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S1Z0
#35: Protein
40SribosomalproteinS7 /
Mass: 23084.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S8C4
#36: Protein
40Sribosomalproteins9-likeprotein / Ribosome
Mass: 22029.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S0Z4
#37: Protein
40SribosomalproteinS13-likeprotein / Ribosome
Mass: 16912.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0RZM9
#38: Protein
40SribosomalproteinS14-likeprotein / Ribosome
Mass: 16071.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SFL1
#39: Protein
40SribosomalproteinS16-likeprotein / Ribosome
Mass: 15962.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SBR7
#40: Protein
40SribosomalproteinS22-likeprotein / Ribosome
Mass: 14905.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SHI0
#41: Protein
40Sribosomalproteins23-likeprotein / Ribosome
Mass: 15934.653 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0RY17
#42: Protein
40SribosomalproteinS28-likeprotein / Ribosome
Mass: 7741.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S9M9
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RNA chain , 2 types, 2 molecules C1C2
#44: RNA chain
35SrRNA
Mass: 749031.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus)
#45: RNA chain
U3snoRNA
Mass: 73966.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus)
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