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

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Basic information

Entry
Database: PDB / ID: 6rxv
TitleCryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state B2
Components
  • (40S ribosomal protein ...) x 15
  • (U3 small nucleolar RNA-associated protein ...) x 2
  • 35S ribosomal RNA
  • Bfr2
  • 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
  • Ribosome biogenesis protein ENP2
  • Rps18
  • Rrp7
  • Rrp9
  • Snu13
  • Sof1
  • U3 small nucleolar ribonucleoprotein protein lcp5-like protein
  • U3 snoRNA
  • UTP10
  • Utp12
  • Utp13
  • Utp14
  • Utp15
  • Utp16
  • Utp17
  • Utp18
  • Utp2
  • Utp20
  • Utp21
  • Utp24
  • Utp3
  • Utp30
  • Utp4
  • Utp5
  • Utp6
  • Utp7
  • Utp8
KeywordsRIBOSOME / ribosome biogenesis / rRNA
Function / homology
Function and homology information


box H/ACA snoRNP complex / tRNA cytidine N4-acetyltransferase activity / rRNA acetylation involved in maturation of SSU-rRNA / 18S rRNA cytidine N-acetyltransferase activity / snRNA pseudouridine synthesis / Noc4p-Nop14p complex / tRNA acetylation / CURI complex / UTP-C complex / t-UTP complex ...box H/ACA snoRNP complex / tRNA cytidine N4-acetyltransferase activity / rRNA acetylation involved in maturation of SSU-rRNA / 18S rRNA cytidine N-acetyltransferase activity / snRNA pseudouridine synthesis / Noc4p-Nop14p complex / tRNA acetylation / CURI complex / UTP-C complex / t-UTP complex / Mpp10 complex / Pwp2p-containing subcomplex of 90S preribosome / rRNA (pseudouridine) methyltransferase activity / histone H2AQ104 methyltransferase activity / box C/D sno(s)RNA 3'-end processing / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methyltransferase activity / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D methylation guide snoRNP complex / positive regulation of rRNA processing / tRNA export from nucleus / rRNA primary transcript binding / sno(s)RNA-containing ribonucleoprotein complex / rRNA base methylation / U3 snoRNA binding / snoRNA binding / preribosome, small subunit precursor / positive regulation of transcription by RNA polymerase I / 90S preribosome / RNA processing / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / RNA endonuclease activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, 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 / cytosolic small ribosomal subunit / nuclear membrane / methylation / tRNA binding / rRNA binding / protein ubiquitination / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / GTPase activity / GTP binding / nucleolus / RNA binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
40S small subunit processome assembly factor 1 / WD repeat-containing protein 75 first beta-propeller / 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 ...40S small subunit processome assembly factor 1 / WD repeat-containing protein 75 first beta-propeller / 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 / Nucleolar protein 10-like, second domain / Nucleolar protein 10-like, N-terminal domain / 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 domain / Small subunit processome component 20 homolog, C-terminal / Ribosomal RNA assembly KRR1 / : / : / : / KRR1 small subunit processome component, second KH 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 / RNA cytidine acetyltransferase NAT10/TcmA, helicase domain / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / GNAT acetyltransferase 2 / Nucleolar protein 14 / Nop14-like family / NOL6/Upt22 / Nrap protein domain 1 / Nrap protein, domain 2 / Nrap protein, domain 3 / Nrap protein, domain 4 / Nrap protein, domain 5 / Nrap protein, domain 6 / 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 / U3 small nucleolar RNA-associated protein 6 / Ribosomal RNA-processing protein 7, C-terminal domain / Ribosomal RNA-processing protein 7 / Rrp7, RRM-like N-terminal domain / U3 small nucleolar RNA-associated protein 4 / : / U3 small nucleolar RNA-associated protein 6 / Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain / Rrp7 RRM-like N-terminal domain / Small-subunit processome, Utp11 / Sof1-like protein / BING4, C-terminal domain / Fcf2 pre-rRNA processing, C-terminal / Fcf2/DNTTIP2 / WD repeat-containing protein WDR46/Utp7 / : / : / Utp11 protein / Sof1-like domain / BING4CT (NUC141) domain / Fcf2 pre-rRNA processing / BING4CT (NUC141) 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 / WDR3 second beta-propeller domain / WDR3 first beta-propeller 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 / HEATR1-like, HEAT repeats / 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
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein s23-like protein / 40S ribosomal protein S6 / 40S ribosomal protein S8 / DDB1- and CUL4-associated factor 13 / Nucleolar protein 58 ...GUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 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 / U three protein 7 / 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 / 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 / Uncharacterized protein / U3 small nucleolar ribonucleoprotein protein lcp5-like protein / 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 / U3 small nucleolar ribonucleoprotein protein IMP3 / 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 S14-like protein / Ribosomal RNA-processing protein / U3 small nucleolar RNA-associated protein 13 C-terminal domain-containing protein / H/ACA ribonucleoprotein complex subunit 2 / rRNA 2'-O-methyltransferase fibrillarin / 40S ribosomal protein S22-like protein / Uncharacterized protein / Uncharacterized protein CTHT_0071780 / Small ribosomal subunit protein eS24
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 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.
History
DepositionJun 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.0Aug 14, 2019Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 14, 2019Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 14, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 14, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Aug 14, 2019Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 14, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 14, 2019Data content type: Primary map / Data content type: Primary map / Provider: 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
Revision 1.2Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Revision 1.1Apr 9, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: database_2 / em_admin / Data content type: EM metadata / EM metadata / EM metadata
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update
Revision 1.3Oct 1, 2025Group: Advisory / Data collection / Derived calculations
Category: em_admin / pdbx_validate_close_contact ...em_admin / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _em_admin.last_update
Revision 1.2Oct 1, 2025Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / Item: _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
UA: Periodic tryptophan protein 2-like protein
UB: Utp2
UC: Utp3
UD: Utp4
UF: Utp6
UG: Utp7
UJ: UTP10
UK: U3 small nucleolar RNA-associated protein 11
UL: Utp12
UM: Utp13
UN: Utp14
UO: Utp15
UQ: Utp17
UR: Utp18
UU: Utp21
UX: Utp24
UZ: Utp30
CA: Nop1
CB: Nop1
CC: Nop56
CD: Nop58
CE: Snu13
CF: Snu13
CG: Rrp9
CH: RNA 3'-terminal phosphate cyclase-like protein
CI: Bms1
CJ: Imp3
CK: Imp4
CL: Mpp10
CM: Sof1
CN: Emg1
CO: Emg1
CP: KRR1 small subunit processome component
CQ: Pre-rRNA-processing protein PNO1
CR: Kre33
CS: Kre33
CT: Fcf2
Ca: 40S ribosomal protein S1
Cb: 40S ribosomal protein S4
Cc: 40S ribosomal protein s5-like protein
Cd: 40S ribosomal protein S6
Ce: 40S ribosomal protein S7
Cf: 40S ribosomal protein S8
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
Ck: 40S ribosomal protein S11-like protein
Cm: 40S ribosomal protein S22-like protein
Cn: 40S ribosomal protein s23-like protein
Co: 40S ribosomal protein S24
Cp: 40S ribosomal protein S28-like protein
CU: Faf1
C1: 35S ribosomal RNA
C2: U3 snoRNA
UV: U3 small nucleolar RNA-associated protein 22
CV: Rrp7
CW: Ribosome biogenesis protein ENP2
UT: Utp20
UH: Utp8
UE: Utp5
US: Noc4
Cl: Rps18
CX: Enp1
CY: U3 small nucleolar ribonucleoprotein protein lcp5-like protein
CZ: Bfr2
UI: Utp5
UP: Utp16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,670,59171
Polymers4,669,97968
Non-polymers6133
Water00
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 , 44 types, 49 molecules UAUBUCUDUFUGUJULUMUNUOUQURUUUXUZCACBCCCDCECFCGCHCICJCKCLCMCN...

#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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
#17: Protein Utp30


Mass: 43700.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0RYF6
#21: Protein Snu13


Mass: 13831.854 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0SG51
#23: 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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0SAY9
#30: 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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0S3V7
#31: 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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0S4E3
#49: Protein Faf1


Mass: 34576.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0S5F1
#53: Protein Rrp7


Mass: 36366.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0SDB8
#54: Protein Ribosome biogenesis protein ENP2


Mass: 75833.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0S902
#55: Protein Utp20


Mass: 295278.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0SHP3
#56: Protein Utp8


Mass: 102421.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: P0CT47
#57: Protein Utp5


Mass: 44663.355 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0RYX2
#58: Protein Noc4


Mass: 63331.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0RZL4
#59: Protein Rps18


Mass: 17826.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0S6J7
#60: Protein Enp1


Mass: 54319.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0S5J4
#61: Protein U3 small nucleolar ribonucleoprotein protein lcp5-like protein


Mass: 42625.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0S7Z2
#62: Protein Bfr2


Mass: 69040.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0SAJ6
#63: Protein Utp16


Mass: 40726.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0S612

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

#8: 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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0SF32
#52: 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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0S2E0

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40S ribosomal protein ... , 15 types, 15 molecules CaCbCcCdCeCfCgChCiCjCkCmCnCoCp

#34: Protein 40S ribosomal protein S1


Mass: 29245.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0S7T8
#35: Protein 40S ribosomal protein S4


Mass: 29800.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0S1A6
#36: Protein 40S ribosomal protein s5-like protein


Mass: 23679.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0S1Z0
#37: Protein 40S ribosomal protein S6


Mass: 27490.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0RY43
#38: Protein 40S ribosomal protein S7


Mass: 23084.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0S8C4
#39: Protein 40S ribosomal protein S8


Mass: 23102.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0RY45
#40: Protein 40S ribosomal protein s9-like protein


Mass: 22029.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0S0Z4
#41: Protein 40S ribosomal protein S13-like protein


Mass: 16912.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0RZM9
#42: Protein 40S ribosomal protein S14-like protein


Mass: 16071.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0SFL1
#43: Protein 40S ribosomal protein S16-like protein


Mass: 15962.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0SBR7
#44: Protein 40S ribosomal protein S11-like protein


Mass: 18698.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0SF00
#45: Protein 40S ribosomal protein S22-like protein


Mass: 14905.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0SHI0
#46: Protein 40S ribosomal protein s23-like protein


Mass: 15934.653 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0RY17
#47: Protein 40S ribosomal protein S24


Mass: 15535.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: P0CU28
#48: Protein 40S ribosomal protein S28-like protein


Mass: 7741.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0S9M9

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RNA chain , 2 types, 2 molecules C1C2

#50: RNA chain 35S ribosomal RNA


Mass: 758475.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
#51: RNA chain U3 snoRNA


Mass: 73966.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)

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Non-polymers , 3 types, 3 molecules

#64: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#65: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#66: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN
Has protein modificationN

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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 B2 / Type: RIBOSOME / Entity ID: #1-#63 / Source: NATURAL
Source (natural)Organism: Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719
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 FIELD
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
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48335 / Symmetry type: POINT

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