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- EMDB-10055: Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaet... -

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Basic information

Entry
Database: EMDB / ID: EMD-10055
TitleCryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state a
Map data
Sample90S pre-ribosome, state a
  • Periodic tryptophan protein 2-like protein
  • Utp2
  • Utp3
  • Utp4
  • Utp6
  • Utp7
  • Utp10
  • (U3 small nucleolar RNA-associated protein ...) x 2
  • Utp12
  • Utp13
  • Utp14
  • Utp15
  • Utp17
  • Utp18
  • Utp21
  • Utp24
  • Utp30
  • Nop1
  • Nop56
  • Nop58
  • Snu13
  • Rrp9
  • RNA 3'-terminal phosphate cyclase-like protein
  • Bms1
  • Imp3
  • Imp4
  • Mpp10
  • Sof1
  • Emg1
  • KRR1 small subunit processome component
  • Pre-rRNA-processing protein PNO1
  • Kre33
  • Fcf2
  • (40S ribosomal protein ...) x 9
  • Faf1
  • (nucleic-acidNucleic acid) x 2
  • Rrp7
  • Utp8
  • Utp5
  • Noc4
  • Rps1840S ribosomal protein S18
  • Enp1
  • Utp16
  • Rrp5
  • ligand
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 / tRNA binding / ribosome / rRNA binding / nucleic acid binding / structural constituent of ribosome / translation / GTPase activity / GTP binding / nucleolus / RNA binding / ATP binding / identical protein binding / nucleus / cytoplasm
Ribosomal protein S4, conserved site / U3 small nucleolar RNA-associated protein 6 / Tetratricopeptide repeat-containing domain / U3 snoRNA associated / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Small-subunit processome, Utp13 / Ribosomal protein S5 domain 2-type fold, subgroup / NOP5, N-terminal ...Ribosomal protein S4, conserved site / U3 small nucleolar RNA-associated protein 6 / Tetratricopeptide repeat-containing domain / U3 snoRNA associated / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Small-subunit processome, Utp13 / Ribosomal protein S5 domain 2-type fold, subgroup / NOP5, N-terminal / Fcf2 pre-rRNA processing, C-terminal / WD40/YVTN repeat-like-containing domain superfamily / Armadillo-type fold / Ribosomal protein L1, 3-layer alpha/beta-sandwich / RNA 3'-terminal phosphate cyclase type 2 / WD40-repeat-containing domain / Nrap protein, domain 4 / NOSIC / BP28, C-terminal domain / Ribosomal protein S13, conserved site / Ribosomal protein S13-like, H2TH / Small-subunit processome, Utp12 / Nucleolar protein 14 / Sof1-like protein / Small-subunit processome, Utp21 / Helicase domain / Bystin / S15/NS1, RNA-binding / Quinoprotein amine dehydrogenase, beta chain-like / BING4, C-terminal domain / Quinoprotein alcohol dehydrogenase-like superfamily / Tetratricopeptide-like helical domain superfamily / U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / Nucleic acid-binding, OB-fold / Ribosomal protein S13/S15, N-terminal / Nucleotide-binding alpha-beta plait domain superfamily / AARP2CN / Ribosomal S11, conserved site / Pyrrolo-quinoline quinone beta-propeller repeat / Small-subunit processome, Utp11 / Helix hairpin bin domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 30s ribosomal protein S13, C-terminal / Protein of unknown function DUF4602 / Possible tRNA binding domain / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein S28e conserved site / tRNA (guanine-N1-)-methyltransferase, N-terminal / Periodic tryptophan protein 2 / Alpha/beta knot methyltransferases / S-adenosyl-L-methionine-dependent methyltransferase / 50S ribosomal protein L30e-like / Bms1/Tsr1-type G domain / TmcA/NAT10/Kre33 / RNA cytidine acetyltransferase NAT10 / Nrap protein domain 1 / Nucleolar complex protein 4 / Ribosomal RNA-processing protein 7, C-terminal domain / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein S7, conserved site / Sas10 C-terminal domain / U3 small nucleolar RNA-associated protein 15, C-terminal / Tetratricopeptide repeat / WD40 repeat, conserved site / G-protein beta WD-40 repeat / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Fibrillarin, conserved site / Ribosomal RNA assembly KRR1 / U3 small nucleolar RNA-associated protein 10, N-terminal / Ribosomal protein S4/S9 / RNA-binding domain, S1 / Ribosomal protein S15P / Ribosomal protein L1-like / RNA 3'-terminal phosphate cyclase domain / Ribosomal protein S7 domain / Sas10/Utp3/C1D / Brix domain / Nrap protein, domain 3 / RNA-binding S4 domain superfamily / GNAT domain / Nrap protein, domain 5 / Nrap protein, domain 6 / Ribosomal protein S8 superfamily / Ribosome biogenesis protein BMS1/TSR1, C-terminal / Nop domain superfamily / WD40-repeat-containing domain superfamily / RNA 3'-terminal phosphate cyclase, insert domain superfamily / K Homology domain, type 1 superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S11 superfamily / RNA 3'-terminal phosphate cyclase domain superfamily / Ribosomal protein S5/S7 / Ribosome biogenesis protein Bms1, N-terminal / 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
Uncharacterized protein / 40S ribosomal protein S7 / Uncharacterized protein / Putative U3 small nucleolar ribonucleoprotein protein / 40S ribosomal protein S28-like protein / Uncharacterized protein / WD_REPEATS_REGION domain-containing protein / 40S ribosomal protein S16-like protein / WD_REPEATS_REGION domain-containing protein / WD_REPEATS_REGION domain-containing protein ...Uncharacterized protein / 40S ribosomal protein S7 / Uncharacterized protein / Putative U3 small nucleolar ribonucleoprotein protein / 40S ribosomal protein S28-like protein / Uncharacterized protein / WD_REPEATS_REGION domain-containing protein / 40S ribosomal protein S16-like protein / WD_REPEATS_REGION domain-containing protein / WD_REPEATS_REGION domain-containing protein / 40S ribosomal protein S22-like protein / S4 RNA-binding domain-containing protein / Uncharacterized protein / Putative U3 small nucleolar ribonucleoprotein / WD_REPEATS_REGION domain-containing protein / U3 small nucleolar RNA-associated protein 11 / Periodic tryptophan protein 2-like protein / 40S ribosomal protein S14-like protein / Uncharacterized protein / WD_REPEATS_REGION domain-containing protein / Ribonucloprotein / Uncharacterized protein / Uncharacterized protein / Putative U3 snoRNP protein / Uncharacterized protein / Uncharacterized protein / 40S ribosomal protein s5-like protein / 40S ribosomal protein s23-like protein / WD_REPEATS_REGION domain-containing protein / Nop domain-containing protein / Utp12 domain-containing protein / WD_REPEATS_REGION domain-containing protein / CBF domain-containing protein / WD_REPEATS_REGION domain-containing protein / 40S ribosomal protein S13-like protein / RNA 3'-terminal phosphate cyclase-like protein / 40S ribosomal protein s9-like protein / RNA cytidine acetyltransferase / Putative ribosomal protein / U3 small nucleolar RNA-associated protein 22 / Putative nucleolar protein / Pre-rRNA-processing protein PNO1 / KRR1 small subunit processome component / Bms1-type G domain-containing protein / Fcf2 domain-containing protein / Sas10 domain-containing protein / Uncharacterized protein / Uncharacterized protein / BP28CT domain-containing protein / Uncharacterized protein / Uncharacterized protein CTHT_0071780
Biological speciesChaetomium thermophilum (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 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 ReportPDB-ID: 6rxy

SummaryFull reportAbout validation report
History
DepositionJun 10, 2019-
Header (metadata) releaseAug 14, 2019-
Map releaseAug 14, 2019-
UpdateOct 2, 2019-
Current statusOct 2, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6rxy
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10055.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 480 pix.
= 520.32 Å
1.08 Å/pix.
x 480 pix.
= 520.32 Å
1.08 Å/pix.
x 480 pix.
= 520.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.084 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.3193684 - 0.4369211
Average (Standard dev.)0.00033813153 (±0.010610348)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 520.32 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0841.0841.084
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z520.320520.320520.320
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.3190.4370.000

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Supplemental data

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Sample components

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Entire 90S pre-ribosome, state a

EntireName: 90S pre-ribosome, state a / Number of components: 56

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Component #1: protein, 90S pre-ribosome, state a

ProteinName: 90S pre-ribosome, state a / Recombinant expression: No
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #2: protein, Periodic tryptophan protein 2-like protein

ProteinName: Periodic tryptophan protein 2-like protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 100.817508 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #3: protein, Utp2

ProteinName: Utp2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 103.960703 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #4: protein, Utp3

ProteinName: Utp3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 73.214633 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #5: protein, Utp4

ProteinName: Utp4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 97.696523 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #6: protein, Utp6

ProteinName: Utp6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 46.924773 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #7: protein, Utp7

ProteinName: Utp7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 63.629379 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #8: protein, Utp10

ProteinName: Utp10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 198.508438 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #9: protein, U3 small nucleolar RNA-associated protein 11

ProteinName: U3 small nucleolar RNA-associated protein 11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.37965 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #10: protein, Utp12

ProteinName: Utp12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 107.573039 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #11: protein, Utp13

ProteinName: Utp13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 100.430352 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #12: protein, Utp14

ProteinName: Utp14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 104.741391 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #13: protein, Utp15

ProteinName: Utp15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 60.524145 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #14: protein, Utp17

ProteinName: Utp17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 105.039695 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #15: protein, Utp18

ProteinName: Utp18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 69.055141 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #16: protein, Utp21

ProteinName: Utp21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 115.122008 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #17: protein, Utp24

ProteinName: Utp24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.135992 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #18: protein, Utp30

ProteinName: Utp30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 43.700527 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #19: protein, Nop1

ProteinName: Nop1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 32.960844 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #20: protein, Nop56

ProteinName: Nop56 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 57.830699 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #21: protein, Nop58

ProteinName: Nop58 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 64.292113 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #22: protein, Snu13

ProteinName: Snu13 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.831854 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #23: protein, Rrp9

ProteinName: Rrp9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 69.610438 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #24: protein, RNA 3'-terminal phosphate cyclase-like protein

ProteinName: RNA 3'-terminal phosphate cyclase-like protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 43.399766 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #25: protein, Bms1

ProteinName: Bms1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 134.17225 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #26: protein, Imp3

ProteinName: Imp3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.802396 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #27: protein, Imp4

ProteinName: Imp4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.216266 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #28: protein, Mpp10

ProteinName: Mpp10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 86.082141 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #29: protein, Sof1

ProteinName: Sof1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 50.869828 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #30: protein, Emg1

ProteinName: Emg1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 27.936164 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #31: protein, KRR1 small subunit processome component

ProteinName: KRR1 small subunit processome component / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.500777 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #32: protein, Pre-rRNA-processing protein PNO1

ProteinName: Pre-rRNA-processing protein PNO1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.715047 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #33: protein, Kre33

ProteinName: Kre33 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 119.795125 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #34: protein, Fcf2

ProteinName: Fcf2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.569129 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #35: protein, 40S ribosomal protein s5-like protein

ProteinName: 40S ribosomal protein s5-like proteinRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.679225 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #36: protein, 40S ribosomal protein S7

ProteinName: 40S ribosomal protein S7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.08465 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #37: protein, 40S ribosomal protein s9-like protein

ProteinName: 40S ribosomal protein s9-like proteinRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.029836 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #38: protein, 40S ribosomal protein S13-like protein

ProteinName: 40S ribosomal protein S13-like proteinRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.912891 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #39: protein, 40S ribosomal protein S14-like protein

ProteinName: 40S ribosomal protein S14-like proteinRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.071464 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #40: protein, 40S ribosomal protein S16-like protein

ProteinName: 40S ribosomal protein S16-like proteinRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.962771 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #41: protein, 40S ribosomal protein S22-like protein

ProteinName: 40S ribosomal protein S22-like proteinRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.905471 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #42: protein, 40S ribosomal protein s23-like protein

ProteinName: 40S ribosomal protein s23-like proteinRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.934653 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #43: protein, 40S ribosomal protein S28-like protein

ProteinName: 40S ribosomal protein S28-like proteinRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.74198 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #44: protein, Faf1

ProteinName: Faf1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.576586 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #45: nucleic-acid, 35S rRNA

nucleic acidName: 35S rRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: GGGGGGAUGU CCGGGUCGCC CUGGGCACCU CUCCGCGGCA GCCUUCGCGG GCAAGCCGUA GUCCCGGUUC AUACGUCGCC GCAAUCGCGA GGGGACCAAC GGGUAACCGU UCCUCCAAGC GGUCGCCGGC GAGCACCACC CCAGCCCCGC CGCCGCCCCC AGCGCACCGC ...Sequence:
GGGGGGAUGU CCGGGUCGCC CUGGGCACCU CUCCGCGGCA GCCUUCGCGG GCAAGCCGUA GUCCCGGUUC AUACGUCGCC GCAAUCGCGA GGGGACCAAC GGGUAACCGU UCCUCCAAGC GGUCGCCGGC GAGCACCACC CCAGCCCCGC CGCCGCCCCC AGCGCACCGC GCGCAGGGGG GCCGGCGCGG CAUCUGGGAA GACUCCUAAG GCGCAAGGGA AUACCCCGUG UGCGCCGGGG GUUGGGCUCU GUGGGUGCUU GGCCGCUGGC CAGACCUACU UCAAAGCCAC CGGGGGUACC UACCGGUUGG GGAAGCCCUA GCGGCUGAAC CUCUCGGUCG GGCCUCCUCU UGGGGCGCCU AGGCGGUGUC UUCGGGUCGC GUGCAGCCUC CCGUCCUCGC CUGCCGACAG CGCUCUGGGG AAUUCAGGAG GGGAAAGCAG AUGUGCCCCG CGGCGAGACU GGCGCACCGC CGGACGAGCU GCUGGGGCAC GCGGGUACGC UAGCCGCUAG CGCCCGCCAG CCUGUAACUA GAGUGAACUC GGCCGCCCUG AAACACGGGC GGUUGGCCUG CUUAGGCGCA CGAUAGUUAC CUGGUUGAUU CUGCCAGUAG UCAUAUGCUU GUCUCAAAGA UUAAGCCAUG CAUGUCUAAG UAUAAGCAAU UAUACAGCGA AACUGCGAAU GGCUCAUUAA AUCAGUUAUC GUUUAUUUGA UAGUACCUUA CUACAUGGAU AACCGUGGUA AUUCUAGAGC UAAUACAUGC UGAAAAUCCC GACUUCGGAA GGGAUGUAUU UAUUAGAUUA AAAACCAAUG CCCUUCGGGG CUUUCUGGUG AUUCAUAAUA ACUUCUCGAA UCGCACGGCC UUGCGCCGGC GAUGGUUCAU UCAAAUUUCU GCCCUAUCAA CUUUCGACGG CUGGGUAUUG GCCAGCCGUG GUGACAACGG GUAACGGAGG GUUAGGGCUC GACCCCGGAG AAGGAGCCUG AGAAACGGCU ACUACAUCCA AGGAAGGCAG CAGGCGCGCA AAUUACCCAA UCCCGACACG GGGAGGUAGU GACAAUAAAU ACUGAUACAG GGCUCUUUCG GGUCUUGUAA UUGGAAUGAG UACAAUUUAA AUCCCUUAAC GAGGAACAAU UGGAGGGCAA GUCUGGUGCC AGCAGCCGCG GUAAUUCCAG CUCCAAUAGC GUAUAUUAAA GUUGUUGAGG UUAAAAAGCU CGUAGUUGAA CCUUGGGCCU AGCCCGCCGG UCCGCCUCAC CGCGUGCACU GGCUGGGCUG GGCCUUUCCU UCUGGAGAAC CGCAUGCCCU UCACUGGGUG UGUCGGGGAA CCAGGACUUU UACUCUGAAC AAAUUAGAUC GCUUAAAGAA GGCCUAUGCU UGAAUACAUU AGCAUGGAAU AAUAGAAUAG GACGUGUGGU UCUAUUUUGU UGGUUUCUAG GACCGCCGUA AUGAUUAAUA GGGACAGUCG GGGGCGUCAG UAUUCAAUUG UCAGAGGUGA AAUUCUUGGA UUUAUUGAAG ACUAACAACU GCGAAAGCAU UCGCCAAGGA UGUUUUCAUU AAUCAGGAAC GAAAGUUAGG GGAUCGAAGA CGAUCAGAUA CCGUCGUAGU CUUAACCAUA AACUAUGCCG AUUAGGGAUC GGACGGCGUU UAUUUUUGAC CCGUUCGGCA CCUUACGAUA AAUCAAAAUG UUUGGGCUCC UGGGGGAGUA UGGUCGCAAG GCUGAAACUU AAAGAAAUUG ACGGAAGGGC ACCACCAGGG GUGGAGCCUG CGGCUUAAUU UGACUCAACA CGGGGAAACU CACCAGGUCC AGACACGAUG AGGAUUGACA GAUUGAGAGC UCUUUCUUGA UUUCGUGGGU GGUGGUGCAU GGCCGUUCUU AGUUGGUGGA GUGAUUUGUC UGCUUAAUUG CGAUAACGAA CGAGACCUUA ACCUGCUAAA UAGCCCGUAU UGCCUUGGCA GUACGCCGGC UUCUUAGAGG GACUAUCGGC UCAAGCCGAU GGAAGUUUGA GGCAAUAACA GGUCUGUGAU GCCCUUAGAU GUUCUGGGCC GCACGCGCGC UACACUGACA GAGCCAGCGA GUACUCCCUU GGCCGAGAGG CCCGGGUAAU CUUGUUAAAC UCUGUCGUGC UGGGGAUAGA GCAUUGCAAU UAUUGCUCUU CAACGAGGAA UCCCUAGUAA GCGCAAGUCA UCAGCUUGCG UUGAUUACGU CCCUGCCCUU UGUACACACC GCCCGUCGCU ACUACCGAUU CGGAAAGUUA UCCAAACUCG GUCGUUUAGA GGAAGUAAAA GUCGUAACAA GGUCUCCGUA GGUGAACCUG CGGAGGGAUC AUU
MassTheoretical: 749.031188 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

+
Component #46: nucleic-acid, U3 snoRNA

nucleic acidName: U3 snoRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: AGCGACAAUA CUUCAGAGAA UCAUUUCUAU AGUAGUUGUC CUCUCUUGUG UUUCCUAAAG GAGCCACAGA UCCCACCCGG GUUGAUGAAC GAGAUCCUCG GCGCCAGUGA GGUCCAUUUA CUCUCGCUCU ACCUGCAAAG GUGGCGGUCG CGUGCCUCGU CUCGCGGCUG ...Sequence:
AGCGACAAUA CUUCAGAGAA UCAUUUCUAU AGUAGUUGUC CUCUCUUGUG UUUCCUAAAG GAGCCACAGA UCCCACCCGG GUUGAUGAAC GAGAUCCUCG GCGCCAGUGA GGUCCAUUUA CUCUCGCUCU ACCUGCAAAG GUGGCGGUCG CGUGCCUCGU CUCGCGGCUG UAUAGAGAGU GGCGAUGAUC UGUACCCCGC GGGGUGGGUG UCGAUGGAAG UCUGACCGGC
MassTheoretical: 73.966539 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

+
Component #47: protein, U3 small nucleolar RNA-associated protein 22

ProteinName: U3 small nucleolar RNA-associated protein 22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 131.105422 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

+
Component #48: protein, Rrp7

ProteinName: Rrp7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 36.36657 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

+
Component #49: protein, Utp8

ProteinName: Utp8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 102.421133 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

+
Component #50: protein, Utp5

ProteinName: Utp5 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 44.663355 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

+
Component #51: protein, Noc4

ProteinName: Noc4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 63.331664 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

+
Component #52: protein, Rps18

ProteinName: Rps1840S ribosomal protein S18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.826707 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

+
Component #53: protein, Enp1

ProteinName: Enp1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 54.319605 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

+
Component #54: protein, Utp16

ProteinName: Utp16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 40.726016 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

+
Component #55: protein, Rrp5

ProteinName: Rrp5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 197.449188 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

+
Component #56: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 28 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 20250
3D reconstructionSoftware: RELION / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

-
Atomic model buiding

Output model

+
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