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

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Basic information

Entry
Database: PDB / ID: 6rxu
TitleCryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state B1
Components
  • (40S ribosomal protein ...) x 15
  • (Putative U3 small nucleolar ...) x 2
  • (U3 small nucleolar ...) x 2
  • 35S rRNA
  • Bfr2
  • Bms1
  • Emg1
  • Enp1
  • Faf1
  • Fcf2
  • Imp3
  • KRR1 small subunit processome component
  • Kre33
  • Noc4
  • Nop1
  • Nop56
  • Nop58
  • Periodic tryptophan protein 2-like protein
  • Pre-rRNA-processing protein PNO1
  • Putative U3 snoRNP protein
  • Putative ribosomal protein
  • RNA 3'-terminal phosphate cyclase-like protein
  • Ribosome biogenesis protein ENP2
  • Rrp9
  • Snu13
  • Sof1
  • U3 snoRNA
  • UTP10
  • Utp12
  • Utp13
  • Utp14
  • Utp15
  • Utp16
  • Utp17
  • Utp18
  • Utp2
  • Utp20
  • Utp24
  • Utp30
  • Utp3
  • Utp4
  • Utp5
  • Utp6
  • Utp7
  • Utp8
KeywordsRIBOSOME / ribosome biogenesis / rRNA
Function / homology
Function and homology information


rRNA cytidine N-acetyltransferase activity / tRNA acetylation / Mpp10 complex / mRNA modification / 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 / Mpp10 complex / mRNA modification / 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 / U3 snoRNA binding / protein localization to nucleolus / rRNA export from nucleus / small nucleolar ribonucleoprotein complex / preribosome, small subunit precursor / 90S preribosome / 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) / snoRNA binding / RNA processing / small-subunit processome / ribosomal small subunit biogenesis / nuclear periphery / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / small ribosomal subunit rRNA binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA processing / catalytic activity / 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
Ribosomal protein L1p/L10e family / RNA 3'-terminal phosphate cyclase, insert domain superfamily / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / S-adenosyl-L-methionine-dependent methyltransferase / 50S ribosomal protein L30e-like / Bms1/Tsr1-type G domain / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / TmcA/NAT10/Kre33 ...Ribosomal protein L1p/L10e family / RNA 3'-terminal phosphate cyclase, insert domain superfamily / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / S-adenosyl-L-methionine-dependent methyltransferase / 50S ribosomal protein L30e-like / Bms1/Tsr1-type G domain / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / TmcA/NAT10/Kre33 / RNA cytidine acetyltransferase NAT10 / Ribosomal protein S8 superfamily / Nop domain superfamily / WD40-repeat-containing domain superfamily / K Homology domain, type 1 superfamily / Ribosomal protein S28e conserved site / Ribosomal protein S7 domain superfamily / Ribosomal protein S11 superfamily / RNA-binding S4 domain superfamily / RNA 3'-terminal phosphate cyclase domain superfamily / Ribosome biogenesis protein Bms1, N-terminal / Ribosomal 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 / Helix hairpin bin domain superfamily / Ribosomal protein L1/ribosomal biogenesis protein / Krr1, KH1 domain / U3 small nucleolar RNA-associated protein 10, N-terminal / Ribosomal protein S3Ae, conserved site / Ribosomal protein S6e, conserved site / Pyrrolo-quinoline quinone beta-propeller repeat / Ribosomal protein L7Ae/L8/Nhp2 family / Sas10 C-terminal domain / U3 small nucleolar RNA-associated protein 15, C-terminal / WD40 repeat, conserved site / 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 / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S4/S9 / Ribosomal protein S15P / Ribosomal protein L1-like / RNA 3'-terminal phosphate cyclase domain / Ribosomal protein S7 domain / Ribosomal RNA assembly KRR1 / AATF leucine zipper-containing domain / Periodic tryptophan protein 2 / Nucleolar complex protein 4 / P-loop containing nucleoside triphosphate hydrolase / 30s ribosomal protein S13, C-terminal / Protein of unknown function DUF4602 / Possible tRNA binding domain / Nucleolar protein 10/Enp2 / Ribosomal protein S4, KOW domain / Ribosomal protein S4e, N-terminal, conserved site / Dip2/Utp12 Family / Ribosomal protein S7e / Ribosomal protein S8e / Ribosomal protein S15 / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S11 / 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 / Nop14-like family / Ribosomal protein S7p/S5e / Sas10 C-terminal domain / U3 small nucleolar RNA-associated protein 6 / BING4CT (NUC141) domain / BP28CT (NUC211) domain / U3 small nucleolar RNA-associated protein 10 / Utp11 protein / Utp13 specific WD40 associated domain / Utp14 protein / UTP15 C terminal / U3 snoRNA associated / CBF/Mak21 family / Down-regulated in metastasis / Utp21 specific WD40 associated putative domain / Ribosomal protein S6e / 40S ribosomal protein S4 C-terminus / Nop, C-terminal domain / Sof1-like domain / Fibrillarin / snoRNA binding domain, fibrillarin / NOP5NT (NUC127) domain
Uncharacterized protein / RNA cytidine acetyltransferase / 40S ribosomal protein s9-like protein / 40S ribosomal protein s5-like protein / 40S ribosomal protein S4 / Putative nucleolar protein / WD_REPEATS_REGION domain-containing protein / RNA 3'-terminal phosphate cyclase-like protein / 40S ribosomal protein S13-like protein / WD_REPEATS_REGION domain-containing protein ...Uncharacterized protein / RNA cytidine acetyltransferase / 40S ribosomal protein s9-like protein / 40S ribosomal protein s5-like protein / 40S ribosomal protein S4 / Putative nucleolar protein / WD_REPEATS_REGION domain-containing protein / RNA 3'-terminal phosphate cyclase-like protein / 40S ribosomal protein S13-like protein / WD_REPEATS_REGION domain-containing protein / CBF domain-containing protein / WD_REPEATS_REGION domain-containing protein / Nop domain-containing protein / WD_REPEATS_REGION domain-containing protein / 40S ribosomal protein S8 / 40S ribosomal protein S6 / 40S ribosomal protein s23-like protein / Utp12 domain-containing protein / KRR1 small subunit processome component / Pre-rRNA-processing protein PNO1 / Periodic tryptophan protein 2-like protein / DRIM domain-containing protein / 40S ribosomal protein S22-like protein / Uncharacterized protein / Ribonucloprotein / WD_REPEATS_REGION domain-containing protein / Uncharacterized protein / 40S ribosomal protein S14-like protein / U3 small nucleolar RNA-associated protein 11 / 40S ribosomal protein S24 / 40S ribosomal protein S11-like protein / WD_REPEATS_REGION domain-containing protein / Putative U3 small nucleolar ribonucleoprotein / Uncharacterized protein / S4 RNA-binding domain-containing protein / WD_REPEATS_REGION domain-containing protein / WD_REPEATS_REGION domain-containing protein / Uncharacterized protein CTHT_0071780 / Uncharacterized protein / 40S ribosomal protein S16-like protein / 40S ribosomal protein S1 / Bms1-type G domain-containing protein / Fcf2 domain-containing protein / Sas10 domain-containing protein / Uncharacterized protein / Uncharacterized protein / BP28CT domain-containing protein / Uncharacterized protein / Uncharacterized protein / 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 / Putative ribosomal protein
Biological speciesChaetomium thermophilum (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 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
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: Putative U3 snoRNP protein
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: 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
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 rRNA
C2: U3 snoRNA
CW: Ribosome biogenesis protein ENP2
UT: Utp20
UH: Utp8
UE: Utp5
US: Noc4
Cl: Putative ribosomal protein
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)4,503,12069
Polymers4,502,50766
Non-polymers6133
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 , 40 types, 45 molecules UAUBUCUDUFUGUJULUMUNUOUQURUUUXUZCACBCCCDCECFCGCHCICJCMCNCOCP...

#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 Utp2


Mass: 103960.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SDW0
#3: Protein Utp3 / /


Mass: 73214.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S4H3
#4: Protein Utp4


Mass: 97696.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SCT7
#5: Protein Utp6 / /


Mass: 46924.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S387
#6: Protein Utp7


Mass: 63629.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0RZ99
#7: Protein UTP10


Mass: 198508.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S5L1
#9: Protein Utp12


Mass: 107573.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0RZL9
#10: Protein Utp13


Mass: 100430.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SG95
#11: Protein Utp14


Mass: 104741.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S8Y4
#12: Protein Utp15 / /


Mass: 60524.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SEI5
#13: Protein Utp17


Mass: 105039.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SCS8
#14: Protein Utp18 / /


Mass: 69055.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SBN9
#15: Protein 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
#16: Protein Utp24


Mass: 22135.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus)
#17: Protein Utp30


Mass: 43700.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S7X0
#18: Protein Nop1


Mass: 32960.844 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SGY2
#19: Protein Nop56


Mass: 57830.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S2U4
#20: Protein Nop58 / /


Mass: 64292.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0RYF6
#21: Protein Snu13


Mass: 13831.854 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SGM0
#22: Protein Rrp9 / /


Mass: 69610.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SG51
#23: Protein 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
#24: Protein Bms1


Mass: 134172.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S445
#25: Protein Imp3 / /


Mass: 21802.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SDL4
#28: Protein Sof1


Mass: 50869.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0RY94
#29: Protein Emg1 / /


Mass: 27936.164 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0SAY9
#30: Protein 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
#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 (fungus) / References: UniProt: G0S3T2
#32: 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
#33: Protein Fcf2


Mass: 22569.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0S4E3
#49: 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
#52: 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
#53: 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
#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 Utp5


Mass: 44663.355 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (fungus) / References: UniProt: G0RYX2
#56: 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
#57: 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
#58: 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
#60: 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
#61: Protein Utp16


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

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U3 small nucleolar ... , 2 types, 2 molecules UKCY

#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 (fungus) / References: UniProt: G0SF32
#59: 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 (fungus) / References: UniProt: G0S7Z2

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

#26: 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
#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) Chaetomium thermophilum (fungus) / References: UniProt: G0S9I7

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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 (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 (fungus) / References: UniProt: G0S1A6
#36: Protein 40S ribosomal protein s5-like protein / Ribosome / Ribosome


Mass: 23679.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (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 (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 (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 (fungus) / References: UniProt: G0RY45
#40: Protein 40S ribosomal protein s9-like protein / Ribosome / Ribosome


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


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


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


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


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


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


Mass: 15934.653 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (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 (fungus) / References: UniProt: P0CU28
#48: Protein 40S ribosomal protein S28-like protein / Ribosome / Ribosome


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

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RNA chain , 2 types, 2 molecules C1C2

#50: RNA chain 35S rRNA


Mass: 758475.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetomium thermophilum (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 (fungus)

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Non-polymers , 3 types, 3 molecules

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


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


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


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

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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 B1 / Type: RIBOSOME
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, ...Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61
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: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 343726 / Symmetry type: POINT

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