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- EMDB-10052: Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaet... -

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Basic information

Entry
Database: EMDB / ID: EMD-10052
TitleCryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state B1
Map data
Sample90S pre-ribosome, state B1
  • Periodic tryptophan protein 2-like protein
  • Utp2
  • Utp3
  • Utp4
  • Utp6
  • Utp7
  • UTP10
  • (U3 small nucleolar ...) x 2
  • Utp12
  • Utp13
  • Utp14
  • Utp15
  • Utp17
  • Utp18
  • Putative U3 snoRNP protein
  • Utp24
  • Utp30
  • Nop1
  • Nop56
  • Nop58
  • Snu13
  • Rrp9
  • RNA 3'-terminal phosphate cyclase-like protein
  • Bms1
  • Imp3
  • (Putative U3 small nucleolar ...) x 2
  • Sof1
  • Emg1
  • KRR1 small subunit processome component
  • Pre-rRNA-processing protein PNO1
  • Kre33
  • Fcf2
  • (40S ribosomal protein ...) x 15
  • Faf1
  • (nucleic-acidNucleic acid) x 2
  • Ribosome biogenesis protein ENP2
  • Utp20
  • Utp8
  • Utp5
  • Noc4
  • Putative ribosomal protein
  • Enp1
  • Bfr2
  • Utp16
  • (ligand) x 3
Function / homology
Function and homology information


rRNA cytidine N-acetyltransferase activity / tRNA acetylation / Mpp10 complex / rRNA (pseudouridine) methyltransferase activity / nuclear microtubule / rRNA modification / endonucleolytic cleavage in 5'-ETS 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) / snRNA binding / box C/D snoRNP complex ...rRNA cytidine N-acetyltransferase activity / tRNA acetylation / Mpp10 complex / rRNA (pseudouridine) methyltransferase activity / nuclear microtubule / rRNA modification / endonucleolytic cleavage in 5'-ETS 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) / snRNA binding / box C/D snoRNP complex / 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 / Transferases, Acyltransferases, Transferring groups other than aminoacyl groups / RNA processing / small-subunit processome / ribosomal small subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear periphery / small ribosomal subunit rRNA binding / methyltransferase activity / small ribosomal subunit / rRNA processing / catalytic activity / ribosome biogenesis / cytosolic small ribosomal subunit / ribonucleoprotein complex / ribosome / rRNA binding / structural constituent of ribosome / translation / GTPase activity / GTP binding / nucleolus / RNA binding / ATP binding / identical protein binding / nucleus / cytoplasm
TmcA/NAT10/Kre33 / RNA 3'-terminal phosphate cyclase, insert domain superfamily / Helix hairpin bin 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 3'-terminal phosphate cyclase, insert domain superfamily / Helix hairpin bin 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 / RNA cytidine acetyltransferase NAT10 / Ribosomal protein S8 superfamily / Nop domain superfamily / WD40-repeat-containing domain superfamily / K Homology domain, type 1 superfamily / Ribosomal protein L1/ribosomal biogenesis protein / 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 / Ribosomal protein S28e conserved site / Ribosomal protein S17, archaeal/eukaryotic / Krr1, KH1 domain / U3 small nucleolar RNA-associated protein 10, N-terminal / 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 / Possible tRNA binding domain / 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 / 40S ribosomal protein S1/3, eukaryotes / Protein of unknown function DUF4602 / Nucleolar protein 10/Enp2 / Ribosomal protein S4, KOW domain / Ribosomal protein S13, conserved site / NUC153 domain / Brix domain / 40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal / Helicase / RNA 3'-terminal phosphate cyclase (RTC), insert domain / Bystin / Down-regulated in metastasis / Ribosomal S13/S15 N-terminal domain / RS4NT (NUC023) domain / AARP2CN (NUC121) domain / BP28CT (NUC211) domain / BING4CT (NUC141) domain / NOP5NT (NUC127) domain / Apoptosis-antagonizing transcription factor, C-terminal / Sof1-like domain / U3 snoRNA associated / Domain of unknown function (DUF1726) / Utp13 specific WD40 associated domain / U3 small nucleolar RNA-associated protein 6 / Fcf2 pre-rRNA processing / Sas10 C-terminal domain / UTP15 C terminal / U3 small nucleolar RNA-associated protein 10 / Apoptosis antagonizing transcription factor / GNAT acetyltransferase 2 / Possible tRNA binding domain / Domain of unknown function (DUF4602) / 40S ribosomal protein S4 C-terminus / Utp21 specific WD40 associated putative domain / Nop14-like family / Nop, C-terminal domain / Ribosomal protein S6e / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S12/S23 / Ribosomal protein S7p/S5e / Ribosomal protein S15 / Ribosomal protein S17
Uncharacterized protein / WD_REPEATS_REGION domain-containing protein / 40S ribosomal protein S16-like protein / Uncharacterized protein / Putative U3 small nucleolar ribonucleoprotein protein / Uncharacterized protein / 40S ribosomal protein S28-like protein / S4 RNA-binding domain-containing protein / Ribosome biogenesis protein ENP2 / Uncharacterized protein ...Uncharacterized protein / WD_REPEATS_REGION domain-containing protein / 40S ribosomal protein S16-like protein / Uncharacterized protein / Putative U3 small nucleolar ribonucleoprotein protein / Uncharacterized protein / 40S ribosomal protein S28-like protein / S4 RNA-binding domain-containing protein / Ribosome biogenesis protein ENP2 / Uncharacterized protein / 40S ribosomal protein S7 / WD_REPEATS_REGION domain-containing protein / DRIM domain-containing protein / Uncharacterized protein / Putative U3 small nucleolar ribonucleoprotein / WD_REPEATS_REGION 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 / Uncharacterized protein / WD_REPEATS_REGION domain-containing protein / Ribonucloprotein / Uncharacterized protein / 40S ribosomal protein S22-like protein / U3 small nucleolar ribonucleoprotein protein lcp5-like protein / Uncharacterized protein CTHT_0071780 / Putative U3 snoRNP protein / Uncharacterized protein / Uncharacterized protein / 40S ribosomal protein S4 / 40S ribosomal protein s23-like protein / 40S ribosomal protein S6 / 40S ribosomal protein S8 / 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 / 40S ribosomal protein s5-like protein / 40S ribosomal protein S1 / RNA cytidine acetyltransferase / 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 / Uncharacterized protein / Uncharacterized protein / Putative ribosomal protein / 40S ribosomal protein S24
Biological speciesChaetomium thermophilum (fungus)
Methodsingle 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 ReportPDB-ID: 6rxu

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

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6rxu
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10052.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: 0.04
Minimum - Maximum-0.23713444 - 0.359036
Average (Standard dev.)0.0005698588 (±0.009769347)
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-0.2370.3590.001

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Supplemental data

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Sample components

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Entire 90S pre-ribosome, state B1

EntireName: 90S pre-ribosome, state B1 / Number of components: 65

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Component #1: protein, 90S pre-ribosome, state B1

ProteinName: 90S pre-ribosome, state B1 / 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, Putative U3 snoRNP protein

ProteinName: Putative U3 snoRNP protein / 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, Putative U3 small nucleolar ribonucleoprotein

ProteinName: Putative U3 small nucleolar ribonucleoprotein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.216266 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #28: protein, Putative U3 small nucleolar ribonucleoprotein protein

ProteinName: Putative U3 small nucleolar ribonucleoprotein protein / 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 S1

ProteinName: 40S ribosomal protein S1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.245158 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #36: protein, 40S ribosomal protein S4

ProteinName: 40S ribosomal protein S4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.800764 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #37: 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 #38: protein, 40S ribosomal protein S6

ProteinName: 40S ribosomal protein S6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.490139 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #39: 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 #40: protein, 40S ribosomal protein S8

ProteinName: 40S ribosomal protein S8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.102416 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #41: 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 #42: 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 #43: 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 #44: 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 #45: protein, 40S ribosomal protein S11-like protein

ProteinName: 40S ribosomal protein S11-like proteinRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.698182 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #46: 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 #47: 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 #48: protein, 40S ribosomal protein S24

ProteinName: 40S ribosomal protein S24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.535286 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

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Component #49: 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 #50: protein, Faf1

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

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Component #51: 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 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 ACUACCGAUC CAGAGAGGUC GGCAACGACC ACUCAGGGCC GGAAAGUUAU CCAAACUCGG UCGUUUAGAG GAAGUAAAAG UCGUAACAAG GUCUCCGUAG GUGAACCUGC GGAGGGAUCA UU
MassTheoretical: 758.475312 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

+
Component #52: 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 UAUAGAGAGU GGCGAUGAUC UGUACCCCGC GGGGUGGGUG UCGAUGGAAG UCUGACCGGC
MassTheoretical: 73.966539 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

+
Component #53: protein, Ribosome biogenesis protein ENP2

ProteinName: Ribosome biogenesis protein ENP2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 75.833805 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

+
Component #54: protein, Utp20

ProteinName: Utp20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 295.278938 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

+
Component #55: protein, Utp8

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

+
Component #56: protein, Utp5

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

+
Component #57: protein, Noc4

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

+
Component #58: protein, Putative ribosomal protein

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

+
Component #59: protein, Enp1

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

+
Component #60: protein, U3 small nucleolar ribonucleoprotein protein lcp5-like p...

ProteinName: U3 small nucleolar ribonucleoprotein protein lcp5-like protein
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 42.625387 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

+
Component #61: protein, Bfr2

ProteinName: Bfr2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 69.040602 kDa
SourceSpecies: Chaetomium thermophilum (fungus)

+
Component #62: protein, Utp16

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

+
Component #63: ligand, ZINC ION

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

+
Component #64: ligand, GUANOSINE-5'-TRIPHOSPHATE

LigandName: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.52318 kDa

+
Component #65: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

-
Experimental details

-
Sample preparation

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

-
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: 343726
3D reconstructionSoftware: RELION / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

-
Atomic model buiding

Output model

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