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- PDB-9xaf: Cryo-EM structure of the 90S pre-ribosome (Enp1-Rrp12 Mut) from C... -

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Basic information

Entry
Database: PDB / ID: 9xaf
TitleCryo-EM structure of the 90S pre-ribosome (Enp1-Rrp12 Mut) from Chaetomium thermophilum, state a
Components
  • (40S ribosomal protein ...) x 8
  • (Nucleolar protein ...) x 2
  • (Small-subunit processome Utp12 domain-containing ...) x 2
  • (U3 small nucleolar RNA-associated protein ...) x 4
  • (U3 small nucleolar ribonucleoprotein protein ...) x 3
  • 35s rna
  • Bms1-type G domain-containing protein
  • Bystin-like protein
  • CCAAT-binding factor domain-containing protein
  • DDB1- and CUL4-associated factor 13
  • Fcf2 pre-rRNA processing C-terminal domain-containing protein
  • H/ACA ribonucleoprotein complex subunit 2
  • KRR1 small subunit processome component
  • Nucleolar complex protein 14
  • Nucleolar essential protein 1
  • Periodic tryptophan protein 2-like protein
  • Pre-rRNA-processing protein PNO1
  • Putative U3 small nucleolar ribonucleoprotein protein
  • Putative U3 snoRNP protein
  • Putative ribosomal protein
  • RNA 3'-terminal phosphate cyclase-like protein
  • RNA cytidine acetyltransferase
  • Ribosomal RNA-processing protein
  • Ribosome biogenesis protein C8F11.04
  • Sas10 C-terminal domain-containing protein
  • Small ribosomal subunit protein eS24
  • U three protein 7
  • U3 snoRNP protein
  • UTP14
  • UTP17
  • UTP18
  • UTP24
  • UTP4
  • faf1
  • rRNA 2'-O-methyltransferase fibrillarin
  • u3 rna
  • utp16
  • utp8
KeywordsRIBOSOME / 90S pre-ribosome / Rrp12 / Enp1 / ribosome biogenesis
Function / homology
Function and homology information


box H/ACA snoRNP complex / snRNA pseudouridine synthesis / tRNA cytidine N4-acetyltransferase activity / rRNA acetylation involved in maturation of SSU-rRNA / 18S rRNA cytidine N-acetyltransferase activity / tRNA acetylation / Noc4p-Nop14p complex / t-UTP complex / Pwp2p-containing subcomplex of 90S preribosome / Mpp10 complex ...box H/ACA snoRNP complex / snRNA pseudouridine synthesis / tRNA cytidine N4-acetyltransferase activity / rRNA acetylation involved in maturation of SSU-rRNA / 18S rRNA cytidine N-acetyltransferase activity / tRNA acetylation / Noc4p-Nop14p complex / t-UTP complex / Pwp2p-containing subcomplex of 90S preribosome / Mpp10 complex / rRNA (pseudouridine) methyltransferase activity / snoRNA guided rRNA 2'-O-methylation / histone H2AQ104 methyltransferase activity / box C/D sno(s)RNA 3'-end processing / rRNA methyltransferase activity / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 / 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 / RNA endonuclease activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / RNA splicing / methyltransferase activity / spliceosomal complex / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / mRNA splicing, via spliceosome / small-subunit processome / mRNA processing / rRNA processing / ribosomal small subunit assembly / ribosome biogenesis / ribosomal small subunit biogenesis / small ribosomal subunit / cytosolic small ribosomal subunit / methylation / nuclear membrane / tRNA binding / rRNA binding / structural constituent of ribosome / protein ubiquitination / ribosome / translation / ribonucleoprotein complex / GTPase activity / GTP binding / nucleolus / RNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
WD repeat-containing protein 75 first beta-propeller / : / Ribosomal RNA assembly KRR1 / : / : / : / KRR1 small subunit processome component, second KH domain / Possible tRNA binding domain / RNA cytidine acetyltransferase NAT10 / Possible tRNA binding domain ...WD repeat-containing protein 75 first beta-propeller / : / 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 / U3 snoRNA associated / U3 snoRNA associated / Sof1-like protein / : / Sof1-like domain / BING4, C-terminal domain / Nucleolar complex protein 4 / WD repeat-containing protein WDR46/Utp7 / BING4CT (NUC141) domain / BING4CT (NUC141) domain / U3 small nucleolar RNA-associated protein 6 / : / U3 small nucleolar RNA-associated protein 6 / U3 small nucleolar RNA-associated protein 4 / Small-subunit processome, Utp11 / Nucleolar protein 14 / Fcf2 pre-rRNA processing, C-terminal / Fcf2/DNTTIP2 / : / Utp11 protein / Nop14-like family / Fcf2 pre-rRNA processing / : / U3 small nucleolar RNA-associated protein 15, C-terminal / UTP15 C terminal / WDR3 second beta-propeller domain / WDR3 first beta-propeller domain / U3 small nucleolar RNA-associated protein 18 / U3 small nucleolar RNA-associated protein 13, C-terminal / Periodic tryptophan protein 2 / Utp13 specific WD40 associated domain / BP28, C-terminal domain / Nucleolar protein 58/56, N-terminal / U3 small nucleolar RNA-associated protein 10, N-terminal / U3 small nucleolar RNA-associated protein 10 / : / BP28CT (NUC211) domain / NOP5NT (NUC127) domain / U3 small nucleolar RNA-associated protein 10 / HEATR1-like, HEAT repeats / BP28CT (NUC211) domain / Sas10 C-terminal domain / : / Sas10 C-terminal domain / Small-subunit processome, Utp12 / Dip2/Utp12 Family / Small-subunit processome, Utp21 / : / Utp21 specific WD40 associated putative domain / WDR36/Utp21 second beta-propeller domain / WDR36/Utp21 first beta-propeller / Ribosome biogenesis protein Bms1, N-terminal / U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / Mpp10 protein / Ribosomal RNA-processing protein Rrp9-like / Sas10/Utp3/C1D / RNA 3'-terminal phosphate cyclase type 2 / Sas10/Utp3/C1D family / RNA 3'-terminal phosphate cyclase / Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase domain / RNA 3'-terminal phosphate cyclase, insert domain superfamily / RNA 3'-terminal phosphate cyclase domain superfamily / Nucleolar protein Nop56/Nop58 / RNA 3'-terminal phosphate cyclase / EMG1/NEP1 methyltransferase / RNA 3'-terminal phosphate cyclase (RTC), insert domain / : / Pre-mRNA-splicing factor Syf1/CNRKL1 N-terminal HAT repeat / rRNA 2'-O-methyltransferase fibrillarin-like / Fibrillarin, conserved site / Fibrillarin / Fibrillarin signature. / Fibrillarin / CCAAT-binding factor / CBF/Mak21 family / Krr1, KH1 domain / Krr1 KH1 domain / Quinoprotein amine dehydrogenase, beta chain-like / Bystin / Bystin / U3 snoRNP protein/Ribosome production factor 1 / :
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein s23-like protein / DDB1- and CUL4-associated factor 13 / Nucleolar protein 58 / Small-subunit processome Utp12 domain-containing protein ...ADENOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein s23-like protein / 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 / RNA 3'-terminal phosphate cyclase-like protein / 40S ribosomal protein s9-like protein / 40S ribosomal protein s5-like protein / RNA cytidine acetyltransferase / 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 / Uncharacterized protein / U3 small nucleolar ribonucleoprotein protein lcp5-like protein / Putative U3 snoRNP protein / 40S ribosomal protein S7 / Putative U3 small nucleolar ribonucleoprotein protein / 40S ribosomal protein S28-like protein / Nucleolar essential protein 1 / Uncharacterized protein / 40S ribosomal protein S16-like 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 / 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 CTHT_0071780 / Small ribosomal subunit protein eS24
Similarity search - Component
Biological speciesThermochaetoides thermophila (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsLau, B. / Li, Y. / Zhu, J. / Fischer, P. / Hong, X. / Yuan, R. / Beckmann, R. / Hurt, E. / Cheng, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Rep / Year: 2026
Title: Nucleoplasmic checkpoint of the 40S ribosomal decoding center maturation.
Authors: Benjamin Lau / Yi Li / Jingyi Zhu / Xianwen Ye / Paulina Fischer / Xiaying Hong / Rui Yuan / Roland Beckmann / Ed Hurt / Jingdong Cheng /
Abstract: The decoding center (DC) is a key ribosomal structure for accurate translation, assembled in a multi-step process that starts on nucleolar pre-ribosomes and ends in the cytoplasm. While late ...The decoding center (DC) is a key ribosomal structure for accurate translation, assembled in a multi-step process that starts on nucleolar pre-ribosomes and ends in the cytoplasm. While late cytoplasmic steps and their checkpoint mechanisms are well characterized, the regulation of early nucleoplasmic DC assembly is unclear. Here, we show that the essential assembly factor Rrp12 plays a central coordinating role. Using Chaetomium thermophilum and cryo-electron microscopy analyses of fifteen pre-40S intermediates, we demonstrate that Rrp12 C terminus truncation: (1) inhibits release of the Utp14-Dhr1 pair, (2) displaces Tsr1, (3) promotes premature stabilization of h28, and (4) prevents h44 formation. These defects impair final 18S rRNA processing and prematurely activate the quality control kinase Rio1. Our results reveal a nucleoplasmic checkpoint during DC formation and establish Rrp12 as a critical regulator ensuring accurate assembly and orderly ribosome maturation.
History
DepositionOct 22, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
UA: Periodic tryptophan protein 2-like protein
UB: Nucleolar complex protein 14
UC: Sas10 C-terminal domain-containing protein
UD: UTP4
UF: U3 snoRNP protein
UG: U three protein 7
UJ: U3 small nucleolar RNA-associated protein 10
UK: U3 small nucleolar RNA-associated protein 11
UL: Small-subunit processome Utp12 domain-containing protein
UM: U3 small nucleolar RNA-associated protein 13 C-terminal domain-containing protein
UN: UTP14
UO: U3 small nucleolar RNA-associated protein 15 C-terminal domain-containing protein
UQ: UTP17
UR: UTP18
UU: Putative U3 snoRNP protein
UX: UTP24
UZ: Ribosome biogenesis protein C8F11.04
CA: rRNA 2'-O-methyltransferase fibrillarin
CB: rRNA 2'-O-methyltransferase fibrillarin
CC: Nucleolar protein 56
CD: Nucleolar protein 58
CE: H/ACA ribonucleoprotein complex subunit 2
CF: H/ACA ribonucleoprotein complex subunit 2
CG: Ribosomal RNA-processing protein
CH: RNA 3'-terminal phosphate cyclase-like protein
CI: Bms1-type G domain-containing protein
CJ: U3 small nucleolar ribonucleoprotein protein IMP3
CK: U3 small nucleolar ribonucleoprotein protein IMP4
CL: Putative U3 small nucleolar ribonucleoprotein protein
CM: DDB1- and CUL4-associated factor 13
CN: Nucleolar essential protein 1
CO: Nucleolar essential protein 1
CP: KRR1 small subunit processome component
CQ: Pre-rRNA-processing protein PNO1
CR: RNA cytidine acetyltransferase
CS: RNA cytidine acetyltransferase
CT: Fcf2 pre-rRNA processing C-terminal domain-containing protein
Cc: 40S ribosomal protein s5-like protein
Ce: 40S ribosomal protein S7
Cg: 40S ribosomal protein s9-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
Co: Small ribosomal subunit protein eS24
Cp: 40S ribosomal protein S28-like protein
CU: faf1
C1: 35s rna
C2: u3 rna
UH: utp8
UE: Small-subunit processome Utp12 domain-containing protein
US: CCAAT-binding factor domain-containing protein
Cl: Putative ribosomal protein
CX: Bystin-like protein
CY: U3 small nucleolar ribonucleoprotein protein lcp5-like protein
UI: Small-subunit processome Utp12 domain-containing protein
UP: utp16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,904,98661
Polymers3,903,94657
Non-polymers1,0404
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 31 types, 35 molecules UAUBUCUDUFUGUNUQURUUUXUZCACBCECFCGCHCICLCMCNCOCPCQCRCSCTCoCU...

#1: Protein Periodic tryptophan protein 2-like protein


Mass: 100897.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SF93
#2: Protein Nucleolar complex protein 14


Mass: 103960.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SDW0
#3: Protein Sas10 C-terminal domain-containing protein


Mass: 73214.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S4H3
#4: Protein UTP4


Mass: 97696.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SCT7
#5: Protein U3 snoRNP protein


Mass: 46924.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S387
#6: Protein U three protein 7


Mass: 63629.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0RZ99
#11: Protein UTP14


Mass: 78070.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus)
#13: Protein UTP17


Mass: 105039.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SCS8
#14: Protein UTP18


Mass: 69135.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SBN9
#15: Protein Putative U3 snoRNP protein


Mass: 115122.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S872
#16: Protein UTP24


Mass: 22135.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus)
#17: Protein Ribosome biogenesis protein C8F11.04


Mass: 43700.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S7X0
#18: Protein rRNA 2'-O-methyltransferase fibrillarin / Histone-glutamine methyltransferase


Mass: 32960.844 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SGY2
#21: Protein H/ACA ribonucleoprotein complex subunit 2 / Nucleolar protein family A member 2


Mass: 13831.854 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SGM0
#22: Protein Ribosomal RNA-processing protein


Mass: 69610.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (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) Thermochaetoides thermophila (fungus) / References: UniProt: G0S0B1
#24: Protein Bms1-type G domain-containing protein


Mass: 134172.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S445
#27: Protein Putative U3 small nucleolar ribonucleoprotein protein


Mass: 86082.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S9I7
#28: Protein DDB1- and CUL4-associated factor 13 / WD repeat and SOF domain-containing protein 1


Mass: 50869.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0RY94
#29: Protein Nucleolar essential protein 1


Mass: 27936.164 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (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) Thermochaetoides thermophila (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) Thermochaetoides thermophila (fungus) / References: UniProt: G0S3T2
#32: Protein RNA cytidine acetyltransferase / 18S rRNA cytosine acetyltransferase


Mass: 119795.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus)
References: UniProt: G0S273, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#33: Protein Fcf2 pre-rRNA processing C-terminal domain-containing protein


Mass: 22569.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S4E3
#41: Protein Small ribosomal subunit protein eS24 / 40S ribosomal protein S24


Mass: 15535.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: P0CU28
#43: Protein faf1


Mass: 34576.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S5F1
#46: Protein utp8


Mass: 102421.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: P0CT47
#48: Protein CCAAT-binding factor domain-containing protein


Mass: 63331.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0RZL4
#49: Protein Putative ribosomal protein


Mass: 17826.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S6J7
#50: Protein Bystin-like protein


Mass: 54319.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S5J4
#52: Protein utp16


Mass: 40726.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S612

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U3 small nucleolar RNA-associated protein ... , 4 types, 4 molecules UJUKUMUO

#7: Protein U3 small nucleolar RNA-associated protein 10


Mass: 198508.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S5L1
#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) Thermochaetoides thermophila (fungus) / References: UniProt: G0SF32
#10: Protein U3 small nucleolar RNA-associated protein 13 C-terminal domain-containing protein


Mass: 100430.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SG95
#12: Protein U3 small nucleolar RNA-associated protein 15 C-terminal domain-containing protein


Mass: 60524.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SEI5

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Small-subunit processome Utp12 domain-containing ... , 2 types, 3 molecules ULUEUI

#9: Protein Small-subunit processome Utp12 domain-containing protein


Mass: 107573.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0RZL9
#47: Protein Small-subunit processome Utp12 domain-containing protein


Mass: 44663.355 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0RYX2

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Nucleolar protein ... , 2 types, 2 molecules CCCD

#19: Protein Nucleolar protein 56


Mass: 57830.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S2U4
#20: Protein Nucleolar protein 58


Mass: 64292.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0RYF6

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U3 small nucleolar ribonucleoprotein protein ... , 3 types, 3 molecules CJCKCY

#25: Protein U3 small nucleolar ribonucleoprotein protein IMP3 / U3 small nucleolar ribonucleoprotein protein imp3


Mass: 21802.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SDL4
#26: Protein U3 small nucleolar ribonucleoprotein protein IMP4


Mass: 34216.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0SE90
#51: 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) Thermochaetoides thermophila (fungus) / References: UniProt: G0S7Z2

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40S ribosomal protein ... , 8 types, 8 molecules CcCeCgCiCjCmCnCp

#34: Protein 40S ribosomal protein s5-like protein


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


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


Mass: 22029.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S0Z4
#37: Protein 40S ribosomal protein S14-like protein


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


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


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


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


Mass: 7741.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus) / References: UniProt: G0S9M9

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RNA chain , 2 types, 2 molecules C1C2

#44: RNA chain 35s rna


Mass: 757825.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus)
#45: RNA chain u3 rna


Mass: 87969.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochaetoides thermophila (fungus)

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Non-polymers , 4 types, 4 molecules

#53: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#54: 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
#55: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#56: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Details

Has ligand of interestN
Has protein modificationY

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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 a / Type: RIBOSOME / Entity ID: #1-#52 / Source: NATURAL
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Buffer solutionpH: 7.4
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 44 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1Gautomatchparticle selection
4RELIONCTF correction
7Cootmodel fitting
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
13RELION3D reconstruction
CTF correctionDetails: Relion / Type: NONE
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 143055 / Symmetry type: POINT
Atomic model buildingPDB-ID: 6RXU

6rxu


Accession code: 6RXU / Source name: PDB / Type: experimental model

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