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- PDB-5oql: Cryo-EM structure of the 90S pre-ribosome from Chaetomium thermophilum -

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Entry
Database: PDB / ID: 5oql
TitleCryo-EM structure of the 90S pre-ribosome from Chaetomium thermophilum
Components
  • (40S ribosomal protein ...) x 15
  • (Putative U3 small nucleolar ...) x 2
  • 35S rRNA
  • Bms1
  • Emg1
  • Faf1
  • Fcf2
  • Imp3
  • KRR1 small subunit processome component
  • Nop1
  • Nop58
  • Periodic tryptophan protein 2-like protein
  • Pre-rRNA-processing protein PNO1
  • Putative U3 snoRNP protein
  • Putative nucleolar proteinNucleolus
  • RNA 3'-terminal phosphate cyclase-like protein
  • RNA cytidine acetyltransferase
  • Rrp9
  • Snu13NHP2L1
  • Sof1
  • U3 small nucleolar RNA-associated protein 11
  • U3 snoRNA
  • Utp10
  • Utp12
  • Utp13
  • Utp14
  • Utp15
  • Utp17
  • Utp18
  • Utp2
  • Utp24
  • Utp30
  • Utp3
  • Utp4
  • Utp6
  • Utp7
KeywordsRIBOSOME / Ribosome biogenesis
Function / homology
Function and homology information


tRNA acetylation / Mpp10 complex / rRNA (pseudouridine) methyltransferase activity / rRNA modification / box C/D methylation guide snoRNP complex / rRNA base methylation / rRNA primary transcript binding / sno(s)RNA-containing ribonucleoprotein complex / N-acetyltransferase activity / S-adenosylmethionine-dependent methyltransferase activity ...tRNA acetylation / Mpp10 complex / rRNA (pseudouridine) methyltransferase activity / rRNA modification / box C/D methylation guide snoRNP complex / rRNA base methylation / rRNA primary transcript binding / sno(s)RNA-containing ribonucleoprotein complex / N-acetyltransferase activity / S-adenosylmethionine-dependent methyltransferase activity / snoRNA binding / RNA nuclease activity / RNA processing / catalytic activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / small-subunit processome / methyltransferase activity / ribosomal small subunit biogenesis / rRNA processing / cytosolic small ribosomal subunit / ribosome biogenesis / methylation / small ribosomal subunit / rRNA binding / protein ubiquitination / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / GTP binding / nucleolus / RNA binding / ATP binding / cytoplasm
Similarity search - Function
Domain of unknown function (DUF4602) / : / : / : / 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 ...Domain of unknown function (DUF4602) / : / : / : / 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 / Helicase / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / GNAT acetyltransferase 2 / Ribosomal RNA assembly KRR1 / Nucleolar protein 14 / Nop14-like family / U3 small nucleolar RNA-associated protein 6 / rRNA-processing protein Fcf1, PIN domain / U3 small nucleolar RNA-associated protein 6 / 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 / rRNA-processing protein Fcf1/Utp23 / Fcf1 / 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 / 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 / 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 / Dip2/Utp12 Family / Sas10/Utp3/C1D / Small-subunit processome, Utp21 / U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / RNA 3'-terminal phosphate cyclase type 2 / Sas10/Utp3/C1D family / Mpp10 protein / Utp21 specific WD40 associated putative domain / Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / EMG1/NEP1 methyltransferase / RNA 3'-terminal phosphate cyclase / 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 / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase (RTC), insert domain / Nucleolar protein Nop56/Nop58 / Krr1, KH1 domain / Krr1 KH1 domain / rRNA 2'-O-methyltransferase fibrillarin-like / Fibrillarin, conserved site / Fibrillarin / Fibrillarin signature. / Fibrillarin / Quinoprotein amine dehydrogenase, beta chain-like / U3 snoRNP protein/Ribosome production factor 1 / Large family of predicted nucleotide-binding domains / Ribosome biogenesis protein BMS1/TSR1, C-terminal / AARP2CN / Bms1/Tsr1-type G domain / Ribosome biogenesis protein Bms1/Tsr1 / 40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal / AARP2CN (NUC121) domain / Bms1-type guanine nucleotide-binding (G) domain profile. / AARP2CN (NUC121) domain / Protein of unknown function (DUF663) / NOSIC / NOSIC (NUC001) domain / Nop domain / Nop domain superfamily / Nop, C-terminal domain / snoRNA binding domain, fibrillarin / Nop domain profile. / H/ACA ribonucleoprotein complex, subunit Nhp2-like / PIN domain / Pyrrolo-quinoline quinone beta-propeller repeat
Similarity search - Domain/homology
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 / BING4 C-terminal domain-containing protein ...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 / BING4 C-terminal 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 / 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 / U3 small nucleolar RNA-associated protein 10 / Small ribosomal subunit protein eS1 / Uncharacterized protein / Putative U3 snoRNP protein / 40S ribosomal protein S7 / Uncharacterized protein / 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 / Uncharacterized protein / Nucleolar complex protein 14 / PIN domain-containing protein / 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 / Ribonucloprotein / rRNA 2'-O-methyltransferase fibrillarin / 40S ribosomal protein S22-like protein / Small ribosomal subunit protein eS24
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsCheng, J. / Kellner, N. / Berninghausen, O. / Hurt, E. / Beckmann, R.
CitationJournal: Nat Struct Mol Biol / Year: 2017
Title: 3.2-Å-resolution structure of the 90S preribosome before A1 pre-rRNA cleavage.
Authors: Jingdong Cheng / Nikola Kellner / Otto Berninghausen / Ed Hurt / Roland Beckmann /
Abstract: The 40S small ribosomal subunit is cotranscriptionally assembled in the nucleolus as part of a large chaperone complex called the 90S preribosome or small-subunit processome. Here, we present the 3.2- ...The 40S small ribosomal subunit is cotranscriptionally assembled in the nucleolus as part of a large chaperone complex called the 90S preribosome or small-subunit processome. Here, we present the 3.2-Å-resolution structure of the Chaetomium thermophilum 90S preribosome, which allowed us to build atomic structures for 34 assembly factors, including the Mpp10 complex, Bms1, Utp14 and Utp18, and the complete U3 small nucleolar ribonucleoprotein. Moreover, we visualized the U3 RNA heteroduplexes with a 5' external transcribed spacer (5' ETS) and pre-18S RNA, and their stabilization by 90S factors. Overall, the structure explains how a highly intertwined network of assembly factors and pre-rRNA guide the sequential, independent folding of the individual pre-40S domains while the RNA regions forming the 40S active sites are kept immature. Finally, by identifying the unprocessed A1 cleavage site and the nearby Utp24 endonuclease, we suggest a proofreading model for regulated 5'-ETS separation and 90S-pre-40S transition.
History
DepositionAug 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 2, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.length_a / _cell.length_b / _cell.length_c
Revision 1.3Oct 23, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB

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Structure visualization

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Assembly

Deposited unit
A: Periodic tryptophan protein 2-like protein
B: Utp2
C: Utp3
D: Utp4
E: Utp6
F: Utp7
G: Utp10
H: U3 small nucleolar RNA-associated protein 11
I: Utp12
J: Utp13
K: Utp14
L: Utp15
M: Utp17
N: Utp18
O: Putative U3 snoRNP protein
P: Utp24
Q: Utp30
R: Nop1
S: Nop1
T: Putative nucleolar protein
U: Nop58
V: Snu13
W: Snu13
X: Rrp9
Y: RNA 3'-terminal phosphate cyclase-like protein
Z: Bms1
a: Imp3
b: Putative U3 small nucleolar ribonucleoprotein
c: Putative U3 small nucleolar ribonucleoprotein protein
d: Sof1
e: Emg1
f: Emg1
g: KRR1 small subunit processome component
h: Pre-rRNA-processing protein PNO1
i: RNA cytidine acetyltransferase
j: RNA cytidine acetyltransferase
k: Fcf2
l: 40S ribosomal protein S1
m: 40S ribosomal protein S4
n: 40S ribosomal protein s5-like protein
o: 40S ribosomal protein S6
p: 40S ribosomal protein S7-like protein
q: 40S ribosomal protein S8
r: 40S ribosomal protein s9-like protein
s: 40S ribosomal protein S13-like protein
t: 40S ribosomal protein S14-like protein
u: 40S ribosomal protein S16-like protein
v: 40S ribosomal protein S11-like protein
w: 40S ribosomal protein S22-like protein
x: 40S ribosomal protein s23-like protein
y: 40S ribosomal protein S24
z: 40S ribosomal protein S28-like protein
0: Faf1
1: 35S rRNA
2: U3 snoRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,735,32556
Polymers3,735,26055
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 32 types, 36 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZadef...

#1: Protein Periodic tryptophan protein 2-like protein / Utp1


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
#8: Protein U3 small nucleolar RNA-associated protein 11 / U3 snoRNA-associated protein 11 / Utp11


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
#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 Putative U3 snoRNP 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: 22267.188 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: G0SE30
#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 Putative nucleolar protein / Nucleolus / 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 / NHP2L1


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 / Rcl1


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
#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 / Dim2


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 RNA cytidine acetyltransferase / 18S rRNA cytosine acetyltransferase / 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

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

#26: Protein Putative U3 small nucleolar ribonucleoprotein / 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 Putative U3 small nucleolar ribonucleoprotein 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

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

#34: Protein 40S ribosomal protein S1 / / eS1


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 / / eS4


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 / Ribosome / uS7


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 / / eS6


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-like protein / Ribosome / eS7


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 / / eS8


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 / Ribosome / uS4


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 / Ribosome / uS15


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 / Ribosome


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 / Ribosome / uS9


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 / Ribosome / eS17


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 / Ribosome / uS8


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 / Ribosome / uS12


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 / / eS24


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 / Ribosome / eS28


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 12

#50: RNA chain 35S rRNA


Mass: 827801.812 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: 87992.648 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 , 1 types, 1 molecules

#52: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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: The 90S Pre-ribosomne / Type: COMPLEX / Entity ID: #1-#51 / Source: NATURAL
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (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: 2.4 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameVersionCategory
1Gautomatch0.5particle selection
4CTFFIND4CTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
10RELION2initial Euler assignment
11RELION2final Euler assignment
12RELION2classification
13RELION23D reconstruction
14PHENIXmodel refinement
15REFMACmodel refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 231121 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007140858
ELECTRON MICROSCOPYf_angle_d1.137198388
ELECTRON MICROSCOPYf_dihedral_angle_d14.15181369
ELECTRON MICROSCOPYf_chiral_restr0.05924284
ELECTRON MICROSCOPYf_plane_restr0.00819361

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