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- EMDB-3847: Cryo-EM structure of the 90S pre-ribosome from Chaetomium thermophilum -

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Basic information

Entry
Database: EMDB / ID: EMD-3847
TitleCryo-EM structure of the 90S pre-ribosome from Chaetomium thermophilum
Map data
SampleThe 90S Pre-ribosomne
  • Periodic tryptophan protein 2-like protein
  • Utp2
  • Utp3
  • Utp4
  • Utp6
  • Utp7
  • Utp10
  • U3 small nucleolar RNA-associated protein 11
  • Utp12
  • Utp13
  • Utp14
  • Utp15
  • Utp17
  • Utp18
  • Putative U3 snoRNP protein
  • Utp24
  • Utp30
  • Nop1
  • Putative nucleolar proteinNucleolus
  • Nop58
  • Snu13NHP2L1
  • 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
  • RNA cytidine acetyltransferase
  • Fcf2
  • (40S ribosomal protein ...) x 15
  • Faf1
  • (nucleic-acidNucleic acid) x 2
  • ligand
Function / homology
Function and homology information


rRNA cytidine N-acetyltransferase activity / tRNA acetylation / mRNA modification / Mpp10 complex / 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 RNP complex ...rRNA cytidine N-acetyltransferase activity / tRNA acetylation / mRNA modification / Mpp10 complex / 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 RNP complex / snRNA binding / rRNA base methylation / protein localization to nucleolus / U3 snoRNA binding / rRNA export from nucleus / sno(s)RNA-containing ribonucleoprotein complex / 90S preribosome / preribosome, small subunit precursor / snoRNA binding / 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) / RNA processing / small-subunit processome / ribosomal small subunit biogenesis / nuclear periphery / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / endoribonuclease activity / catalytic activity / small ribosomal subunit rRNA binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA processing / mRNA processing / methyltransferase activity / ribosome biogenesis / cytosolic small ribosomal subunit / ribonucleoprotein complex / small ribosomal subunit / tRNA binding / methylation / rRNA binding / ribosome / structural constituent of ribosome / protein ubiquitination / translation / GTPase activity / GTP binding / nucleolus / RNA binding / ATP binding / identical protein binding / nucleus / cytoplasm
WD40/YVTN repeat-like-containing domain superfamily / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / BING4, C-terminal domain / BP28, C-terminal domain / NOP5, N-terminal / NOSIC / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / RNA 3'-terminal phosphate cyclase, insert domain / Ribosomal protein S4e, N-terminal / Ribosomal protein L23/L15e core domain superfamily ...WD40/YVTN repeat-like-containing domain superfamily / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / BING4, C-terminal domain / BP28, C-terminal domain / NOP5, N-terminal / NOSIC / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / RNA 3'-terminal phosphate cyclase, insert domain / Ribosomal protein S4e, N-terminal / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein S4e, central region / Small-subunit processome, Utp13 / U3 small nucleolar RNA-associated protein 6 / Ribosomal protein S6, eukaryotic / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / Fcf2 pre-rRNA processing, C-terminal / AARP2CN / Ribosomal protein S13/S15, N-terminal / Armadillo-type fold / Nucleolar protein 14 / Small-subunit processome, Utp14 / rRNA-processing protein Fcf1/Utp23 / Ribosome biogenesis protein BMS1/TSR1, C-terminal / Brix domain / Small-subunit processome, Utp11 / Sas10/Utp3/C1D / Small-subunit processome, Utp12 / Sof1-like protein / Nucleic acid-binding, OB-fold / Small-subunit processome, Utp21 / Helicase domain / S15/NS1, RNA-binding / Quinoprotein amine dehydrogenase, beta chain-like / Quinoprotein alcohol dehydrogenase-like superfamily / Tetratricopeptide-like helical domain superfamily / U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / 50S ribosomal protein L30e-like / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein S5/S7, eukaryotic/archaeal / P-loop containing nucleoside triphosphate hydrolase / 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 / Periodic tryptophan protein 2 / 40S ribosomal protein S1/3, eukaryotes / U3 small nucleolar RNA-associated protein 10, N-terminal / Possible tRNA binding domain / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein S28e conserved site / Helix hairpin bin domain superfamily / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Fibrillarin, conserved site / RNA 3'-terminal phosphate cyclase type 2 / Pyrrolo-quinoline quinone beta-propeller repeat / WD40-repeat-containing domain / Ribosomal protein S4, conserved site / Ribosomal S24e conserved site / Ribosomal S11, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein S7, conserved site / 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 S12/S23 / Ribosomal protein S4/S9, eukaryotic/archaeal / S-adenosyl-L-methionine-dependent methyltransferase / RNA-binding S4 domain superfamily / 40S ribosomal protein S11, N-terminal / TmcA/NAT10/Kre33 / Ribosomal protein S23, eukaryotic/archaeal / RNA cytidine acetyltransferase NAT10 / Ribosomal protein S8 superfamily / 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 / Bms1/Tsr1-type G domain / Ribosome biogenesis protein Bms1, N-terminal / Ribosomal protein S4e, central domain superfamily / Ribosomal RNA-processing protein Rrp9-like / Ribosome biogenesis protein Bms1/Tsr1 / Fcf2/DNTTIP2 / Pre-rRNA-processing protein PNO1-like
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 / S4 RNA-binding domain-containing protein / Uncharacterized protein / PINc domain-containing 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 / S4 RNA-binding domain-containing protein / Uncharacterized protein / PINc domain-containing protein / WD_REPEATS_REGION domain-containing protein / Putative U3 small nucleolar ribonucleoprotein / 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 / Histone-glutamine methyltransferase / 40S ribosomal protein S22-like protein / 40S ribosomal protein S7 / Uncharacterized protein / 40S ribosomal protein s5-like protein / Putative U3 snoRNP protein / 40S ribosomal protein S4 / 40S ribosomal protein s23-like protein / 40S ribosomal protein S6 / 40S ribosomal protein S8 / DDB1- and CUL4-associated factor 13 / Nucleolar protein 58 / WD_REPEATS_REGION 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 / Uncharacterized protein / Nucleolar protein 58 / Uncharacterized 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 / U3 small nucleolar RNA-associated protein 10 / 40S ribosomal protein S1 / 40S ribosomal protein S24
Biological speciesChaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Methodsingle 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.
Validation ReportSummary, Full report, XML, About validation report
History
Header (metadata) releaseJul 19, 2017-
DepositionAug 12, 2017-
Map releaseOct 11, 2017-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing 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
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  • 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-5oql
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5oql
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_3847.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: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.3247096 - 0.5959159
Average (Standard dev.)0.00035213277 (±0.0108130425)
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-0.3250.5960.000

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Supplemental data

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Sample components

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Entire The 90S Pre-ribosomne

EntireName: The 90S Pre-ribosomne / Number of components: 53

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Component #1: protein, The 90S Pre-ribosomne

ProteinName: The 90S Pre-ribosomne / Recombinant expression: No
SourceSpecies: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)

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Component #17: protein, Utp24

ProteinName: Utp24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.267188 kDa
SourceSpecies: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)

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Component #20: protein, Putative nucleolar protein

ProteinName: Putative nucleolar proteinNucleolus / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 57.830699 kDa
SourceSpecies: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)

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Component #22: protein, Snu13

ProteinName: Snu13NHP2L1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.831854 kDa
SourceSpecies: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)

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Component #33: protein, RNA cytidine acetyltransferase

ProteinName: RNA cytidine acetyltransferase / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 119.795125 kDa
SourceSpecies: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)

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Component #39: protein, 40S ribosomal protein S7-like protein

ProteinName: 40S ribosomal protein S7-like proteinRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.08465 kDa
SourceSpecies: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)

+
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 (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)

+
Component #50: protein, Faf1

ProteinName: Faf1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.576586 kDa
SourceSpecies: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 ...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 GAACGGCUCA GUGAGGCUUU CGGACUGGCC CAGAGAGGUC GGCAACGACC ACUCAGGGCC GGAAAGUUAU CCAAACUCGG UCGUUUAGAG GAAGUAAAAG UCGUAACAAG GUCUCCGUAG GUGAACCUGC GGAGGGAUCA UUAAUGAGUU ACCACAACUC CCAAACCCAU UGUGAACCUA CCCUUCACGU UGCUUCGGCG GGUCGGGCGC UGUGCCGCCC CUCCGGGCGA CCCGGGGCUC CCCAAAGGCC CCGGGCCCGC CGCCCGCCGG AGGUACGCAA ACUCUUGUUC AUUGUACGGC CUCUCUGAGU GAAGUACUGA AUAAGUCA
MassTheoretical: 827.801812 kDa
SourceSpecies: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (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 GCGCCCAACA GUGAGGUCCA UUAUUUACUC UCGCUCUACC UGCAAAGGUG GCGGUCGCGU GCCUCGUCUC ...Sequence:
AGCGACAAUA CUUCAGAGAA UCAUUUCUAU AGUAGUUGUC CUCUCUUGUG UUUCCUAAAG GAGCCACAGA UCCCACCCGG GUUGAUGAAC GAGAUCCUCG GCGCCCAACA GUGAGGUCCA UUAUUUACUC UCGCUCUACC UGCAAAGGUG GCGGUCGCGU GCCUCGUCUC GCGGCUGUAU AGAGAGUGGC GAUGAUCUGU ACCCCGGCUU UCCUGAGGUC UUGCCUUCGG GCGCUCAGGC GGGGUGGGUG UCGAUGGAAG UCUGACCGGC CAUU
MassTheoretical: 87.992648 kDa
SourceSpecies: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)

+
Component #53: 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

-
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: 2.4 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 / Number of projections: 231121
3D reconstructionSoftware: RELION / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

-
Atomic model buiding

Output model

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