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- EMDB-11357: Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cere... -

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Basic information

Entry
Database: EMDB / ID: EMD-11357
TitleCryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state A (Poly-Ala)
Map data
Sample90S pre-ribbosome state A
  • Periodic tryptophan protein 2
  • (Nucleolar complex protein ...) x 2
  • Something about silencing protein 10
  • (U3 small nucleolar RNA-associated protein ...) x 16
  • Bud site selection protein 21
  • NET1-associated nuclear protein 1
  • (rRNA-processing protein ...) x 2
  • (Ribosome biogenesis protein ...) x 2
  • rRNA 2'-O-methyltransferase fibrillarin
  • (Nucleolar protein ...Nucleolus) x 2
  • 13 kDa ribonucleoprotein-associated protein
  • (Ribosomal RNA-processing protein ...) x 2
  • (U3 small nucleolar ribonucleoprotein protein ...) x 2
  • RNA 3'-terminal phosphate cyclase-like protein
  • Ribosomal RNA small subunit methyltransferase NEP1
  • Essential nuclear protein 1
  • Pre-rRNA-processing protein PNO1
  • Protein FAF1
  • KRR1 small subunit processome component
  • Protein SOF1
  • Regulator of rDNA transcription protein 14
  • (40S ribosomal protein ...) x 11
  • Rps5p
  • (nucleic-acidNucleic acid) x 3
  • (ligand) x 3
Function / homology
Function and homology information


Noc4p-Nop14p complex / CURI complex / t-UTP complex / UTP-C complex / Pwp2p-containing subcomplex of 90S preribosome / sno(s)RNA processing / RNA fragment catabolic process / rRNA small subunit pseudouridine methyltransferase Nep1 / histone-glutamine methyltransferase activity / box C/D RNA 3'-end processing ...Noc4p-Nop14p complex / CURI complex / t-UTP complex / UTP-C complex / Pwp2p-containing subcomplex of 90S preribosome / sno(s)RNA processing / RNA fragment catabolic process / rRNA small subunit pseudouridine methyltransferase Nep1 / histone-glutamine methyltransferase activity / box C/D RNA 3'-end processing / Mpp10 complex / rRNA methyltransferase activity / rRNA (pseudouridine) methyltransferase activity / septum digestion after cytokinesis / rRNA 2'-O-methylation / rRNA modification / regulation of transcription by RNA polymerase I / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of RNA binding / nuclear microtubule / rDNA heterochromatin / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA primary transcript binding / box C/D RNP complex / snRNA binding / positive regulation of transcription by RNA polymerase I / rRNA base methylation / single-stranded telomeric DNA binding / protein localization to nucleolus / U4 snRNA binding / histone glutamine methylation / U3 snoRNA binding / Cul4-RING E3 ubiquitin ligase complex / poly(A)+ mRNA export from nucleus / rRNA export from nucleus / sno(s)RNA-containing ribonucleoprotein complex / tRNA export from nucleus / precatalytic spliceosome / 90S preribosome / preribosome, small subunit precursor / O-methyltransferase activity / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / rRNA methylation / 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) / maturation of SSU-rRNA / U4/U6 x U5 tri-snRNP complex / regulation of translational fidelity / small-subunit processome / ribosomal small subunit biogenesis / proteasome assembly / nuclear periphery / maturation of LSU-rRNA / Cajal body / establishment of cell polarity / endoribonuclease activity / maintenance of translational fidelity / positive regulation of translational fidelity / enzyme activator activity / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA 5'-UTR binding / rRNA processing / mRNA splicing, via spliceosome / cytoplasmic translation / Transferases; Transferring one-carbon groups; Methyltransferases / ribosome biogenesis / unfolded protein binding / cytosolic small ribosomal subunit / small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / cell cycle / ATPase / GTPase activity / mRNA binding / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Nucleic acid-binding, OB-fold / Zinc-binding ribosomal protein / Sas10/Utp3/C1D / Small-subunit processome, Utp12 / Nucleolar protein 14 / Sof1-like protein / Small-subunit processome, Utp21 / Bystin / S15/NS1, RNA-binding / Ribosomal protein S13-like, H2TH ...Nucleic acid-binding, OB-fold / Zinc-binding ribosomal protein / Sas10/Utp3/C1D / Small-subunit processome, Utp12 / Nucleolar protein 14 / Sof1-like protein / Small-subunit processome, Utp21 / Bystin / S15/NS1, RNA-binding / Ribosomal protein S13-like, H2TH / Quinoprotein alcohol dehydrogenase-like superfamily / Tetratricopeptide-like helical domain superfamily / Brix domain / U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / Ribosomal protein S13/S15, N-terminal / Nucleotide-binding alpha-beta plait domain superfamily / AARP2CN / BING4, C-terminal domain / BP28, C-terminal domain / NOP5, N-terminal / NOSIC / U3 snoRNA associated / Small-subunit processome, Utp11 / Ribosome biogenesis protein BMS1/TSR1, C-terminal / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / ATPase, AAA-type, core / WD40 repeat / Ribosomal protein S13 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S11 / H/ACA ribonucleoprotein complex, subunit Nhp2, eukaryote / Nop domain / PIN domain / RNA-binding S4 domain / HAT (Half-A-TPR) repeat / Ribosomal protein L7Ae conserved site / rRNA-processing protein Fcf1/Utp23 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / K Homology domain / Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / NOL6/Upt22 / CCAAT-binding factor / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S12/S23 / Small-subunit processome, Utp14 / RNA 3'-terminal phosphate cyclase, insert domain / Small-subunit processome, Utp13 / Ribosomal protein S9 / 30s ribosomal protein S13, C-terminal / Ribosomal protein L1-like / RNA 3'-terminal phosphate cyclase domain / Ribosomal protein S7 domain / Ribosomal RNA assembly KRR1 / Ribosomal RNA-processing protein 7, C-terminal domain / Anaphase-promoting complex subunit 4, WD40 domain / Periodic tryptophan protein 2 / Nucleolar complex protein 4 / P-loop containing nucleoside triphosphate hydrolase / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S4/S9 / 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 / PIN-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase / 50S ribosomal protein L30e-like / Bms1/Tsr1-type G domain / Regulator of rDNA transcription 14 / Ribosomal protein S15P / U3 small nucleolar RNA-associated protein 10, N-terminal / U3 small nucleolar RNA-associated protein 6 / Ribosomal protein S3Ae, conserved site / Ribosomal protein S5 domain 2-type fold, subgroup / Fcf2 pre-rRNA processing, C-terminal / WD40/YVTN repeat-like-containing domain superfamily / Armadillo-type fold / RNA 3'-terminal phosphate cyclase type 2 / WD40-repeat-containing domain / Ribosomal protein S4, conserved site / Ribosomal S11, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / HEAT, type 2 / U3 small nucleolar RNA-associated protein 8 / Sas10 C-terminal domain / U3 small nucleolar RNA-associated protein 15, C-terminal / WD40 repeat, 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 / RNA 3'-terminal phosphate cyclase-like, conserved site / Fibrillarin, conserved site / Ribosomal protein S3Ae / Fibrillarin / Nrap protein, domain 2
U3 small nucleolar RNA-associated protein 15 / U3 small nucleolar RNA-associated protein 13 / rRNA-processing protein FCF1 / U3 small nucleolar RNA-associated protein 14 / U3 small nucleolar RNA-associated protein 8 / U3 small nucleolar RNA-associated protein 5 / NET1-associated nuclear protein 1 / U3 small nucleolar RNA-associated protein 6 / U3 small nucleolar ribonucleoprotein protein IMP4 / Ribosomal RNA small subunit methyltransferase NEP1 ...U3 small nucleolar RNA-associated protein 15 / U3 small nucleolar RNA-associated protein 13 / rRNA-processing protein FCF1 / U3 small nucleolar RNA-associated protein 14 / U3 small nucleolar RNA-associated protein 8 / U3 small nucleolar RNA-associated protein 5 / NET1-associated nuclear protein 1 / U3 small nucleolar RNA-associated protein 6 / U3 small nucleolar ribonucleoprotein protein IMP4 / Ribosomal RNA small subunit methyltransferase NEP1 / U3 small nucleolar RNA-associated protein 21 / 40S ribosomal protein S28-A / Ribosomal RNA-processing protein 9 / Nucleolar complex protein 4 / U3 small nucleolar RNA-associated protein 4 / RNA 3'-terminal phosphate cyclase-like protein / Bud site selection protein 21 / Ribosome biogenesis protein BMS1 / rRNA-processing protein FCF2 / Something about silencing protein 10 / U3 small nucleolar RNA-associated protein 12 / Nucleolar protein 56 / Nucleolar protein 58 / U3 small nucleolar RNA-associated protein MPP10 / Nucleolar complex protein 14 / U3 small nucleolar RNA-associated protein 22 / Protein SOF1 / U3 small nucleolar RNA-associated protein 10 / 40S ribosomal protein S5 / 40S ribosomal protein S9-A / 40S ribosomal protein S13 / 40S ribosomal protein S14-A / 40S ribosomal protein S22-A / 40S ribosomal protein S23-A / 40S ribosomal protein S16-A / 40S ribosomal protein S18-A / rRNA 2'-O-methyltransferase fibrillarin / Ribosomal RNA-processing protein 7 / KRR1 small subunit processome component / Periodic tryptophan protein 2 / 40S ribosomal protein S7-A / Protein FAF1 / U3 small nucleolar ribonucleoprotein protein IMP3 / 40S ribosomal protein S1-A / U3 small nucleolar RNA-associated protein 11 / 40S ribosomal protein S27-A / Ribosome biogenesis protein UTP30 / Essential nuclear protein 1 / U3 small nucleolar RNA-associated protein 9 / 13 kDa ribonucleoprotein-associated protein / U3 small nucleolar RNA-associated protein 7 / U3 small nucleolar RNA-associated protein 18 / Regulator of rDNA transcription protein 14 / Pre-rRNA-processing protein PNO1
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Baker's yeast (baker's yeast) / Saccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsCheng J / Lau B / Venuta GL / Berninghausen O / Hurt E / Beckmann R
CitationJournal: Science / Year: 2020
Title: 90 pre-ribosome transformation into the primordial 40 subunit.
Authors: Jingdong Cheng / Benjamin Lau / Giuseppe La Venuta / Michael Ameismeier / Otto Berninghausen / Ed Hurt / Roland Beckmann /
Abstract: Production of small ribosomal subunits initially requires the formation of a 90 precursor followed by an enigmatic process of restructuring into the primordial pre-40 subunit. We elucidate this ...Production of small ribosomal subunits initially requires the formation of a 90 precursor followed by an enigmatic process of restructuring into the primordial pre-40 subunit. We elucidate this process by biochemical and cryo-electron microscopy analysis of intermediates along this pathway in yeast. First, the remodeling RNA helicase Dhr1 engages the 90 pre-ribosome, followed by Utp24 endonuclease-driven RNA cleavage at site A, thereby separating the 5'-external transcribed spacer (ETS) from 18 ribosomal RNA. Next, the 5'-ETS and 90 assembly factors become dislodged, but this occurs sequentially, not en bloc. Eventually, the primordial pre-40 emerges, still retaining some 90 factors including Dhr1, now ready to unwind the final small nucleolar U3-18 RNA hybrid. Our data shed light on the elusive 90 to pre-40 transition and clarify the principles of assembly and remodeling of large ribonucleoproteins.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionJul 9, 2020-
Header (metadata) releaseSep 23, 2020-
Map releaseSep 23, 2020-
UpdateSep 30, 2020-
Current statusSep 30, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
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  • Surface view colored by radius
  • Surface level: 0.01
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  • Surface view with fitted model
  • Atomic models: PDB-6zqa
  • Surface level: 0.01
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_11357.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.)
1.06 Å/pix.
x 480 pix.
= 508.32 Å
1.06 Å/pix.
x 480 pix.
= 508.32 Å
1.06 Å/pix.
x 480 pix.
= 508.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.059 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.035635985 - 0.061933927
Average (Standard dev.)0.00030636968 (±0.0024216238)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 508.32 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0591.0591.059
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z508.320508.320508.320
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ100115122
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.0360.0620.000

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Supplemental data

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Sample components

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Entire 90S pre-ribbosome state A

EntireName: 90S pre-ribbosome state A / Number of components: 61

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Component #1: protein, 90S pre-ribbosome state A

ProteinName: 90S pre-ribbosome state A / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Component #2: protein, Periodic tryptophan protein 2

ProteinName: Periodic tryptophan protein 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 104.097039 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #3: protein, Nucleolar complex protein 14

ProteinName: Nucleolar complex protein 14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 94.463195 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #4: protein, Something about silencing protein 10

ProteinName: Something about silencing protein 10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 70.364398 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #5: protein, U3 small nucleolar RNA-associated protein 4

ProteinName: U3 small nucleolar RNA-associated protein 4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 87.909242 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #6: protein, U3 small nucleolar RNA-associated protein 5

ProteinName: U3 small nucleolar RNA-associated protein 5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 72.079445 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #7: protein, U3 small nucleolar RNA-associated protein 6

ProteinName: U3 small nucleolar RNA-associated protein 6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 52.495277 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #8: protein, U3 small nucleolar RNA-associated protein 7

ProteinName: U3 small nucleolar RNA-associated protein 7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 62.41857 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #9: protein, U3 small nucleolar RNA-associated protein 8

ProteinName: U3 small nucleolar RNA-associated protein 8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 80.269648 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #10: protein, U3 small nucleolar RNA-associated protein 9

ProteinName: U3 small nucleolar RNA-associated protein 9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 65.347254 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #11: protein, U3 small nucleolar RNA-associated protein 10

ProteinName: U3 small nucleolar RNA-associated protein 10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 200.298984 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #12: protein, U3 small nucleolar RNA-associated protein 11

ProteinName: U3 small nucleolar RNA-associated protein 11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.806348 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #13: protein, U3 small nucleolar RNA-associated protein 12

ProteinName: U3 small nucleolar RNA-associated protein 12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 106.481133 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #14: protein, U3 small nucleolar RNA-associated protein 13

ProteinName: U3 small nucleolar RNA-associated protein 13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 91.132562 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #15: protein, U3 small nucleolar RNA-associated protein 14

ProteinName: U3 small nucleolar RNA-associated protein 14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 103.18975 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #16: protein, U3 small nucleolar RNA-associated protein 15

ProteinName: U3 small nucleolar RNA-associated protein 15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 57.765289 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #17: protein, Bud site selection protein 21

ProteinName: Bud site selection protein 21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.431016 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #18: protein, NET1-associated nuclear protein 1

ProteinName: NET1-associated nuclear protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 101.341734 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #19: protein, U3 small nucleolar RNA-associated protein 18

ProteinName: U3 small nucleolar RNA-associated protein 18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 66.49425 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #20: protein, Nucleolar complex protein 4

ProteinName: Nucleolar complex protein 4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 63.707844 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #21: protein, U3 small nucleolar RNA-associated protein 21

ProteinName: U3 small nucleolar RNA-associated protein 21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 104.927844 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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

ProteinName: U3 small nucleolar RNA-associated protein 22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 140.660141 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #23: protein, rRNA-processing protein FCF1

ProteinName: rRNA-processing protein FCF1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.650729 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #24: protein, Ribosome biogenesis protein UTP30

ProteinName: Ribosome biogenesis protein UTP30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.668939 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #25: protein, rRNA 2'-O-methyltransferase fibrillarin

ProteinName: rRNA 2'-O-methyltransferase fibrillarin / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 34.525418 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #26: protein, Nucleolar protein 56

ProteinName: Nucleolar protein 56Nucleolus / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 56.961152 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #27: protein, Nucleolar protein 58

ProteinName: Nucleolar protein 58Nucleolus / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 57.060344 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #28: protein, 13 kDa ribonucleoprotein-associated protein

ProteinName: 13 kDa ribonucleoprotein-associated protein / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.582855 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #29: protein, Ribosomal RNA-processing protein 9

ProteinName: Ribosomal RNA-processing protein 9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 65.146969 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #30: protein, U3 small nucleolar ribonucleoprotein protein IMP3

ProteinName: U3 small nucleolar ribonucleoprotein protein IMP3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.928529 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #31: protein, U3 small nucleolar ribonucleoprotein protein IMP4

ProteinName: U3 small nucleolar ribonucleoprotein protein IMP4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.536168 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #32: protein, U3 small nucleolar RNA-associated protein MPP10

ProteinName: U3 small nucleolar RNA-associated protein MPP10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 67.042492 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #33: protein, Ribosome biogenesis protein BMS1

ProteinName: Ribosome biogenesis protein BMS1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 135.792281 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #34: protein, RNA 3'-terminal phosphate cyclase-like protein

ProteinName: RNA 3'-terminal phosphate cyclase-like protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 40.220559 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #35: protein, Ribosomal RNA-processing protein 7

ProteinName: Ribosomal RNA-processing protein 7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.526441 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #36: protein, Ribosomal RNA small subunit methyltransferase NEP1

ProteinName: Ribosomal RNA small subunit methyltransferase NEP1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 27.936461 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #37: protein, Essential nuclear protein 1

ProteinName: Essential nuclear protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 55.207422 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #38: protein, Pre-rRNA-processing protein PNO1

ProteinName: Pre-rRNA-processing protein PNO1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.380623 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #39: protein, rRNA-processing protein FCF2

ProteinName: rRNA-processing protein FCF2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.68924 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #40: protein, Protein FAF1

ProteinName: Protein FAF1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 38.961512 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #41: protein, KRR1 small subunit processome component

ProteinName: KRR1 small subunit processome component / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.226254 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #42: protein, Protein SOF1

ProteinName: Protein SOF1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 56.888918 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #43: protein, Regulator of rDNA transcription protein 14

ProteinName: Regulator of rDNA transcription protein 14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.898289 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #44: protein, 40S ribosomal protein S1-A

ProteinName: 40S ribosomal protein S1-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.798467 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #45: protein, Rps5p

ProteinName: Rps5p / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.0726 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #46: protein, 40S ribosomal protein S7-A

ProteinName: 40S ribosomal protein S7-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.658209 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #47: protein, 40S ribosomal protein S9-A

ProteinName: 40S ribosomal protein S9-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.487893 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #48: protein, 40S ribosomal protein S13

ProteinName: 40S ribosomal protein S13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.059945 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #49: protein, 40S ribosomal protein S14-A

ProteinName: 40S ribosomal protein S14-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.562655 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #50: protein, 40S ribosomal protein S16-A

ProteinName: 40S ribosomal protein S16-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.87749 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #51: protein, 40S ribosomal protein S18-A

ProteinName: 40S ribosomal protein S18-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.071641 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #52: protein, 40S ribosomal protein S22-A

ProteinName: 40S ribosomal protein S22-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.650062 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #53: protein, 40S ribosomal protein S23-A

ProteinName: 40S ribosomal protein S23-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.073896 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #54: protein, 40S ribosomal protein S27-A

ProteinName: 40S ribosomal protein S27-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.893391 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #55: protein, 40S ribosomal protein S28-A

ProteinName: 40S ribosomal protein S28-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.605847 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #56: nucleic-acid, 5ETS RNA

nucleic acidName: 5ETS RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: AUGCGAAAGC AGUUGAAGAC AAGUUCGAAA AGAGUUUGGA AACGAAUUCG AGUAGGCUUG UCGUUCGUUA UGUUUUUGUA AAUGGCCUCG UCAAACGGUG GAGAGAGUCG CUAGGUGAUC GUCAGAUCUG CCUAGUCUCU AUACAGCGUG UUUAAUUGAC AUGGGUUGAU ...Sequence:
AUGCGAAAGC AGUUGAAGAC AAGUUCGAAA AGAGUUUGGA AACGAAUUCG AGUAGGCUUG UCGUUCGUUA UGUUUUUGUA AAUGGCCUCG UCAAACGGUG GAGAGAGUCG CUAGGUGAUC GUCAGAUCUG CCUAGUCUCU AUACAGCGUG UUUAAUUGAC AUGGGUUGAU GCGUAUUGAG AGAUACAAUU UGGGAAGAAA UUCCCAGAGU GUGUUUCUUU UGCGUUUAAC CUGAACAGUC UCAUCGUGGG CAUCUUGCGA UUCCAUUGGU GAGCAGCGAA GGAUUUGGUG GAUUACUAGC UAAUAGCAAU CUAUUUCAAA GAAUUCAAAC UUGGGGGAAU GCCUUGUUGA AUAGCCGGUC GCAAGACUGU GAUUCUUCAA GUGUAACCUC CUCUCAAAUC AGCGAUAUCA AACGUACCAU UCCGUGAAAC ACCGGGGUAU CUGUUUGGUG GAACCUGAUU AGAGGAAACU CAAAGAGUGC UAUGGUAUGG UGACGGAGUG CGCUGGUCAA GAGUGUAAAA GCUUUUUGAA CAGAGAGCAU UUCCGGCAGC AGAGAGACCU GAAAAAGCAA UUUUUCUGGA AUUUCAGCUG UUUCCAAACU CAAUAAGUAU CUUCUAGCAA GAGGGAAUAG GUGGGAAAAA AAAAAAGAGA UUUCGGUUUC UUUCUUUUUU ACUGCUUGUU GCUUCUUCUU UUAAGAUAGU
MassTheoretical: 225.543094 kDa
SourceSpecies: Saccharomyces cerevisiae S288C (yeast)

+
Component #57: nucleic-acid, 18S rRNA

nucleic acidName: 18S rRNA18S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: AAGAUAGUUA UCUGGUUGAU CCUGCCAGUC AUAUGCUUGU CUCAAGACAA UAAAUAACGA UACAGGGCCC AUUCGGGUCU UGUAAUUGGA AUGAGUACAA UGUAAAUACC UUAACGAGGA ACAAUUGGAG GGCAAGUCUG GUGCCAGCAG CCGCGGUAAU UCCAGCUCCA ...Sequence:
AAGAUAGUUA UCUGGUUGAU CCUGCCAGUC AUAUGCUUGU CUCAAGACAA UAAAUAACGA UACAGGGCCC AUUCGGGUCU UGUAAUUGGA AUGAGUACAA UGUAAAUACC UUAACGAGGA ACAAUUGGAG GGCAAGUCUG GUGCCAGCAG CCGCGGUAAU UCCAGCUCCA AUAGCGUAUA UUAAAGUUGU UGCAGUUAAA AAGCUCGUAG UUGAACUUUG GGCCCGGUUG GCCGGUCCGA UUUUUUCGUG UACUGGAUUU CCAACGGGGC CUUUCCUUCU GGCUAACCUU GAGUCCUUGU GGCUCUUGGC GAACCAGGAC UUUUACUUUG AAAAAAUUAG AGUGUUCAAA GCAGGCGUAU UGCUCGAAUA UAUUAGCAUG GAAUAAUAGA AUAGGACGUU UGGUUCUAUU UUGUUGGUUU CUAGGACCAU CGUAAUGAUU AAUAGGGACG GUCGGGGGCA UCAGUAUUCA AUUGUCAGAG GUGAAAUUCU UGGAUUUAUU GAAGACUAAC UACUGCGAAA GCAUUUGCCA AGGACGUUUU CAUUAAUCAA GAACGAAAGU UAGGGGAUCG AAGAUGAUCA GAUACCGUCG UAGUCUUAAC CAUAAACUAU GCCGACUAGG GAUCGGGUGG UGUUUUUUUA AUGACCCACU CGGCACCUUA CGAGAAAUCA AAGUCUUUGG GUUCUGGGGG GAGUAUGGUC GCAAGGCUGA AACUUAAAGG AAUUGACGGA AGGGCACCAC CAGGAGUGGA GCCUGCGGCU UAAUUUGACU CAACACGGGG AAACUCACCA GGUCCAGACA CAAUAAGGAU UGACAGAUUG AGAGCUCUUU CUUGAUUUUG UGGGUGGUGG UGCAUGGCCG UUCUUAGUUG GUGGAGUGAU UUGUCUGCUU AAUUGCGAUA ACGAACGAGA CCUUAACCUA CUAAAUAGUG GUGCUAGCAU UUGCUGGUUA UCCACUUCUU AGAGGGACUA UCGGUUUCAA GCCGAUGGAA GUUUGAGGCA AUAACAGGUC UGUGAUGCCC UUAGACGUUC UGGGCCGCAC GCGCGCUACA CUGACGGAGC CAGCGAGUCU AACCUUGGCC GAGAGGUCUU GGUAAUCUUG UGAAACUCCG UCGUGCUGGG GAUAGAGCAU UGUAAUUAUU GCUCUUCAAC GAGGAAUUCC UAGUAAGCGC AAGUCAUCAG CUUGCGUUGA UUACGUCCCU GCCCUUUGUA CACACCGCCC GUCGCUAGUA CCGAUUGAAU GGCUUAGUGA GGCCUCAGGA UCUGCUUAGA GAAGGGGGCA ACUCCAUCUC AGAGCGGAGA AUUUGGACAA ACUUGGUCAU UUAGAGGAAC UAAAAGUCGU AACAAGGUUU CCGUAGGUGA ACCUGCGGAA GGAUCAUUA
MassTheoretical: 444.436406 kDa
SourceSpecies: Saccharomyces cerevisiae S288C (yeast)

+
Component #58: nucleic-acid, U3 snoRNA

nucleic acidName: U3 snoRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUCGACGUAC UUCAUAGGAU CAUUUCUAUA GGAAUCGUCA CUCUUUGACU CUUCAAAAGA GCCACUGAAU CCAACUUGGU UGAUGAGUCC CAUAACCUUU GUACCCGUGA GAAAGUGCCG UUGCUAUGGC GCGAUGAUCU ACCCAUGGGU GGGUACAAAU GGCAGUCUGA CAAGU
MassTheoretical: 56.132156 kDa
SourceSpecies: Saccharomyces cerevisiae S288C (yeast)

+
Component #59: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

+
Component #60: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

+
Component #61: ligand, GUANOSINE-5'-TRIPHOSPHATE

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

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
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: 44 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 11194
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Euler angles: Relion
FSC plot (resolution estimation)

-
Atomic model buiding

Output model

+
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