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- PDB-6rxx: Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaet... -

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Basic information

Entry
Database: PDB / ID: 6rxx
TitleCryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state C, Poly-Ala
Components
  • (40S ribosomal protein ...) x 16
  • (Putative U3 small nucleolar ...) x 2
  • (U3 small nucleolar RNA-associated protein ...) x 2
  • 35S ribosomal RNA
  • Bfr2
  • 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
  • Ribosomal protein s27-like proteinRibosome
  • Ribosome biogenesis protein ENP2
  • Rrp7
  • Rrp9
  • Snu13
  • Sof1
  • U3 snoRNA
  • UTP10
  • Utp12
  • Utp13
  • Utp14
  • Utp15
  • Utp16
  • Utp17
  • Utp18
  • Utp2
  • Utp20
  • Utp24
  • Utp3
  • Utp4
  • Utp5
  • Utp6
  • Utp7
  • Utp8
KeywordsRIBOSOME / 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 snoRNP 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 snoRNP complex / snRNA binding / rRNA base methylation / protein localization to nucleolus / U3 snoRNA binding / rRNA export from nucleus / small nucleolar ribonucleoprotein complex / preribosome, small subunit precursor / 90S preribosome / 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 / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / ribosomal small subunit biogenesis / nuclear periphery / small ribosomal subunit rRNA binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / catalytic activity / rRNA processing / methyltransferase activity / ribosome biogenesis / cytosolic small ribosomal subunit / small ribosomal subunit / ribonucleoprotein complex / methylation / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / GTPase activity / GTP binding / nucleolus / RNA binding / ATP binding / identical protein binding / nucleus / cytoplasm
Nrap protein domain 6 / Ribosome biogenesis protein Bms1, N-terminal / Nrap protein, domain 3 / Nrap protein, domain 4 / Nrap protein, domain 5 / Nrap protein, domain 6 / Ribosomal protein S8 superfamily / Nop domain superfamily / WD40-repeat-containing domain superfamily / Winged helix DNA-binding domain superfamily ...Nrap protein domain 6 / Ribosome biogenesis protein Bms1, N-terminal / Nrap protein, domain 3 / Nrap protein, domain 4 / Nrap protein, domain 5 / Nrap protein, domain 6 / Ribosomal protein S8 superfamily / Nop domain superfamily / WD40-repeat-containing domain superfamily / Winged helix DNA-binding 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 / Ribosomal protein S19e domain superfamily / Nrap protein domain 1 / Ribosomal protein S4e, central domain superfamily / Protein AATF/Bfr2 / 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 / Nucleolar protein 10/Enp2 / Ribosomal RNA-processing protein 7 / Rrp7, RRM-like N-terminal domain / Krr1, KH1 domain / Ribosomal protein S4, KOW domain / Nop, C-terminal domain / Nrap protein, domain 2 / RNA cytidine acetyltransferase NAT10 / Fibrillarin / AATF leucine zipper-containing domain / 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 S7, conserved site / Fibrillarin, conserved site / U3 small nucleolar RNA-associated protein 10, N-terminal / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S4/S9 / Ribosomal protein S15P / 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 / TmcA/NAT10/Kre33 / Helix hairpin bin domain superfamily / 40S ribosomal protein S11, N-terminal / 40S ribosomal protein S4, C-terminal domain / Bms1/Tsr1-type G domain / S-adenosyl-L-methionine-dependent methyltransferase / Alpha/beta knot methyltransferases / tRNA (guanine-N1-)-methyltransferase, N-terminal / Ribosomal protein S28e conserved site / Nucleolar complex protein 4 / Ribosomal protein S17, archaeal/eukaryotic / Possible tRNA binding domain / Protein of unknown function DUF4602 / 40S ribosomal protein S1/3, eukaryotes / 30s ribosomal protein S13, C-terminal / P-loop containing nucleoside triphosphate hydrolase / Nucleotidyltransferase superfamily / snoRNA binding domain, fibrillarin / U3 small nucleolar RNA-associated protein 15, C-terminal / U3 small nucleolar RNA-associated protein 6 / Ribosomal protein S9/S16 / Ribosomal protein S17 / Ribosomal_S17 N-terminal / Ribosomal protein S13/S18 / Ribosomal protein S8 / Ribosomal protein S12/S23 / Ribosomal protein S24e / Ribosomal protein S28e / Ribosomal protein S27 / Ribosomal protein S19e / Dip2/Utp12 Family / Nop14-like family / Sas10/Utp3/C1D family / Sas10 C-terminal domain / BING4CT (NUC141) domain / Ribosomal S13/S15 N-terminal domain / Down-regulated in metastasis / Nrap protein PAP/OAS1-like domain 5 / Nrap protein nucleotidyltransferase domain 4 / Nrap protein domain 3 / Nrap protein PAP/OAS-like domain / Nrap protein domain 1 / Utp21 specific WD40 associated putative domain / CBF/Mak21 family / BP28CT (NUC211) domain / U3 snoRNA associated / UTP15 C terminal / Utp14 protein / Utp13 specific WD40 associated domain
U3 small nucleolar RNA-associated protein 22 / DDB1- and CUL4-associated factor 13 / 40S ribosomal protein s23-like protein / 40S ribosomal protein S6 / 40S ribosomal protein S8 / RNA cytidine acetyltransferase / 40S ribosomal protein s5-like protein / 40S ribosomal protein S4 / Ribosomal protein s27-like protein / Utp12 domain-containing protein ...U3 small nucleolar RNA-associated protein 22 / DDB1- and CUL4-associated factor 13 / 40S ribosomal protein s23-like protein / 40S ribosomal protein S6 / 40S ribosomal protein S8 / RNA cytidine acetyltransferase / 40S ribosomal protein s5-like protein / 40S ribosomal protein S4 / Ribosomal protein s27-like protein / Utp12 domain-containing protein / 40S ribosomal protein s9-like protein / RNA 3'-terminal phosphate cyclase-like protein / 40S ribosomal protein S13-like protein / Nucleolar protein 58 / WD_REPEATS_REGION domain-containing protein / CBF domain-containing protein / WD_REPEATS_REGION domain-containing protein / Putative U3 small nucleolar ribonucleoprotein / Nucleolar protein 58 / 40S ribosomal protein S22-like protein / WD_REPEATS_REGION domain-containing protein / Uncharacterized protein / S4 RNA-binding domain-containing protein / Uncharacterized protein / 40S ribosomal protein S24 / Uncharacterized protein CTHT_0071780 / DRIM domain-containing protein / Histone-glutamine methyltransferase / 40S ribosomal protein S16-like protein / Ribonucloprotein / WD_REPEATS_REGION domain-containing protein / Uncharacterized protein / 40S ribosomal protein S14-like protein / 40S ribosomal protein S19-like protein / Periodic tryptophan protein 2-like protein / U3 small nucleolar RNA-associated protein 11 / 40S ribosomal protein S11-like protein / WD_REPEATS_REGION domain-containing protein / WD_REPEATS_REGION domain-containing protein / WD_REPEATS_REGION domain-containing protein / U3 small nucleolar RNA-associated protein 10 / 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 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Putative ribosomal protein / 40S ribosomal protein S1 / 40S ribosomal protein S7 / Uncharacterized protein / Ribosome biogenesis protein ENP2 / Putative U3 small nucleolar ribonucleoprotein protein / 40S ribosomal protein S28-like protein / Protein BFR2 / Putative U3 snoRNP protein
Biological speciesChaetomium thermophilum (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.1 Å
AuthorsCheng, J. / Kellner, N. / Griesel, S. / Berninghausen, O. / Beckmann, R. / Hurt, E.
CitationJournal: 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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJun 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
UA: Periodic tryptophan protein 2-like protein
UC: Utp3
UF: Utp6
UG: Utp7
UK: U3 small nucleolar RNA-associated protein 11
UL: Utp12
UM: Utp13
UN: Utp14
UR: Utp18
UU: Putative U3 snoRNP protein
UX: Utp24
CJ: Imp3
CK: Putative U3 small nucleolar ribonucleoprotein
CL: Putative U3 small nucleolar ribonucleoprotein protein
CM: Sof1
CN: Emg1
CO: Emg1
CP: KRR1 small subunit processome component
CQ: Pre-rRNA-processing protein PNO1
Ca: 40S ribosomal protein S1
Cc: 40S ribosomal protein s5-like protein
Ce: 40S ribosomal protein S7
Cg: 40S ribosomal protein s9-like protein
Ch: 40S ribosomal protein S13-like protein
Ci: 40S ribosomal protein S14-like protein
Cj: 40S ribosomal protein S16-like protein
Cm: 40S ribosomal protein S22-like protein
Cn: 40S ribosomal protein s23-like protein
Cp: 40S ribosomal protein S28-like protein
Cq: Ribosomal protein s27-like protein
CU: Faf1
C1: 35S ribosomal RNA
UV: U3 small nucleolar RNA-associated protein 22
CV: Rrp7
Cl: Putative ribosomal protein
CH: RNA 3'-terminal phosphate cyclase-like protein
CI: Bms1
CR: Kre33
CS: Kre33
Cb: 40S ribosomal protein S4
Cd: 40S ribosomal protein S6
Cf: 40S ribosomal protein S8
Ck: 40S ribosomal protein S11-like protein
Co: 40S ribosomal protein S24
CW: Ribosome biogenesis protein ENP2
UT: Utp20
CZ: Bfr2
UB: Utp2
UD: Utp4
UJ: UTP10
UO: Utp15
UQ: Utp17
CX: Enp1
UI: Utp5
UP: Utp16
UH: Utp8
UE: Utp5
US: Noc4
CA: Nop1
CB: Nop1
CC: Putative nucleolar protein
CD: Nop58
CE: Snu13
CF: Snu13
CG: Rrp9
CT: Fcf2
C2: U3 snoRNA
Cr: 40S ribosomal protein S19-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,451,28970
Polymers4,451,15868
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 41 types, 46 molecules UAUCUFUGULUMUNURUUUXCJCMCNCOCPCQCqCUCVClCHCICRCSCWUTCZUBUDUJ...

#1: Protein Periodic tryptophan protein 2-like protein


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 Utp3 /


Mass: 73214.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S4H3
#3: 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
#4: 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
#6: 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
#7: 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
#8: 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
#9: 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
#10: Protein Putative U3 snoRNP protein


Mass: 115122.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S872
#11: Protein Utp24


Mass: 22135.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus)
#12: 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
#15: 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
#16: 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
#17: Protein KRR1 small subunit processome component / / 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
#18: Protein Pre-rRNA-processing protein PNO1


Mass: 28715.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S3T2
#29: Protein Ribosomal protein s27-like protein / Ribosome


Mass: 8923.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S1S4
#30: 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
#33: 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
#34: Protein Putative ribosomal protein /


Mass: 17826.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S6J7
#35: Protein RNA 3'-terminal phosphate cyclase-like protein


Mass: 43399.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S0B1
#36: 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
#37: Protein Kre33 / 18S rRNA cytosine acetyltransferase


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
#43: Protein Ribosome biogenesis protein ENP2 /


Mass: 75833.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S902
#44: Protein Utp20 /


Mass: 295278.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SHP3
#45: Protein Bfr2


Mass: 69040.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SAJ6
#46: 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
#47: 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
#48: 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
#49: 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
#50: 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
#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 Utp5


Mass: 44663.355 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0RYX2
#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 Utp8


Mass: 102421.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: P0CT47
#55: 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
#56: 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
#57: Protein Putative nucleolar protein / Nucleolus


Mass: 57830.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S2U4
#58: 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
#59: Protein Snu13


Mass: 13831.854 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SGM0
#60: 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
#61: 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

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U3 small nucleolar RNA-associated protein ... , 2 types, 2 molecules UKUV

#5: Protein U3 small nucleolar RNA-associated protein 11 / 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
#32: Protein U3 small nucleolar RNA-associated protein 22


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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Putative U3 small nucleolar ... , 2 types, 2 molecules CKCL

#13: Protein Putative U3 small nucleolar ribonucleoprotein


Mass: 34216.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SE90
#14: Protein Putative U3 small nucleolar ribonucleoprotein protein


Mass: 86082.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S9I7

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40S ribosomal protein ... , 16 types, 16 molecules CaCcCeCgChCiCjCmCnCpCbCdCfCkCoCr

#19: Protein 40S ribosomal protein S1 /


Mass: 29245.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S7T8
#20: Protein 40S ribosomal protein s5-like protein / Ribosome


Mass: 23679.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S1Z0
#21: Protein 40S ribosomal protein S7 /


Mass: 23084.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S8C4
#22: Protein 40S ribosomal protein s9-like protein / Ribosome


Mass: 22029.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S0Z4
#23: Protein 40S ribosomal protein S13-like protein / Ribosome


Mass: 16912.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0RZM9
#24: Protein 40S ribosomal protein S14-like protein / Ribosome


Mass: 16071.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SFL1
#25: Protein 40S ribosomal protein S16-like protein / Ribosome


Mass: 15962.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SBR7
#26: Protein 40S ribosomal protein S22-like protein / Ribosome


Mass: 14905.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SHI0
#27: Protein 40S ribosomal protein s23-like protein / Ribosome


Mass: 15934.653 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0RY17
#28: Protein 40S ribosomal protein S28-like protein / Ribosome


Mass: 7741.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S9M9
#38: Protein 40S ribosomal protein S4 /


Mass: 29800.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S1A6
#39: Protein 40S ribosomal protein S6 /


Mass: 27490.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0RY43
#40: Protein 40S ribosomal protein S8 /


Mass: 23102.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0RY45
#41: Protein 40S ribosomal protein S11-like protein / Ribosome


Mass: 18698.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SF00
#42: Protein 40S ribosomal protein S24 /


Mass: 15535.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: P0CU28
#63: Protein 40S ribosomal protein S19-like protein / Ribosome


Mass: 17151.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SFK8

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RNA chain , 2 types, 2 molecules C1C2

#31: RNA chain 35S ribosomal RNA /


Mass: 599293.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus)
#62: RNA chain U3 snoRNA


Mass: 74578.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus)

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Non-polymers , 1 types, 2 molecules

#64: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 90S pre-ribosome, state C / Type: RIBOSOME / Entity ID: #1-#63 / Source: NATURAL
Source (natural)Organism: Chaetomium thermophilum (fungus)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 28 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameCategory
4RELIONCTF correction
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9041 / Symmetry type: POINT

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