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- EMDB-6696: Cryo-EM structure of the 90S small subunit pre-ribosome (Mtr4-dep... -

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Basic information

Entry
Database: EMDB / ID: EMD-6696
TitleCryo-EM structure of the 90S small subunit pre-ribosome (Mtr4-depleted, Enp1-TAP)
Map data
Sample90S small subunit pre-ribosome (Mtr4-depleted, Enp1-TAP)
  • (nucleic-acidNucleic acid) x 3
  • rRNA 2'-O-methyltransferase fibrillarin
  • (Nucleolar protein ...Nucleolus) x 2
  • (Ribosomal RNA-processing protein ...) x 2
  • 13 kDa ribonucleoprotein-associated protein
  • Utp4
  • Utp5
  • Utp8
  • Utp9
  • (U3 small nucleolar RNA-associated protein ...) x 6
  • Utp15
  • Utp17
  • (Ribosome biogenesis protein ...) x 2
  • Periodic tryptophan protein 2
  • Ribosomal RNA small subunit methyltransferase NEP1
  • Enp2
  • KRR1 small subunit processome component
  • (U3 small nucleolar ribonucleoprotein protein ...) x 2
  • Mpp10,U3 small nucleolar RNA-associated protein MPP10
  • Pre-rRNA-processing protein PNO1
  • RNA 3'-terminal phosphate cyclase-like protein
  • Sof1
  • (40S ribosomal protein ...) x 16
  • Utp7
  • Utp11
  • rRNA-processing protein FCF1
  • (Helical domain ...) x 2
  • Unassigned helices
Function / homology
Function and homology information


CURI complex / sno(s)RNA processing / RNA fragment catabolic process / rRNA small subunit pseudouridine methyltransferase Nep1 / t-UTP complex / UTP-C complex / Pwp2p-containing subcomplex of 90S preribosome / histone-glutamine methyltransferase activity / box C/D RNA 3'-end processing / Mpp10 complex ...CURI complex / sno(s)RNA processing / RNA fragment catabolic process / rRNA small subunit pseudouridine methyltransferase Nep1 / t-UTP complex / UTP-C complex / Pwp2p-containing subcomplex of 90S preribosome / histone-glutamine methyltransferase activity / box C/D RNA 3'-end processing / Mpp10 complex / septum digestion after cytokinesis / rRNA methyltransferase activity / rRNA (pseudouridine) methyltransferase activity / rRNA modification / rRNA 2'-O-methylation / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of transcription by RNA polymerase I / nuclear microtubule / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of RNA binding / rDNA heterochromatin / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / snRNA binding / rRNA primary transcript binding / box C/D RNP complex / positive regulation of transcription by RNA polymerase I / rRNA base methylation / single-stranded telomeric DNA binding / protein localization to nucleolus / sno(s)RNA-containing ribonucleoprotein complex / histone glutamine methylation / U4 snRNA binding / SUMOylation of RNA binding proteins / U3 snoRNA binding / rRNA export from nucleus / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / tRNA export from nucleus / 90S preribosome / O-methyltransferase activity / preribosome, small subunit precursor / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / precatalytic spliceosome / Major pathway of rRNA processing in the nucleolus and cytosol / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / snoRNA binding / L13a-mediated translational silencing of Ceruloplasmin expression / rRNA methylation / 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) / regulation of translational fidelity / maturation of SSU-rRNA / U4/U6 x U5 tri-snRNP complex / small-subunit processome / proteasome assembly / ribosomal small subunit biogenesis / nuclear periphery / maturation of LSU-rRNA / Cajal body / establishment of cell polarity / endoribonuclease activity / enzyme activator activity / translational termination / maintenance of translational fidelity / positive regulation of translational fidelity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / mRNA 5'-UTR binding / rRNA processing / mRNA splicing, via spliceosome / cytoplasmic stress granule / cytoplasmic translation / Transferases; Transferring one-carbon groups; Methyltransferases / unfolded protein binding / ribosome biogenesis / small ribosomal subunit / cytosolic small ribosomal subunit / ribosome / rRNA binding / structural constituent of ribosome / translation / ATP hydrolysis activity / GTPase activity / mRNA binding / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ribosomal RNA assembly KRR1 / rRNA-processing protein Fcf1, PIN domain / Nrap protein nucleotidyltransferase domain 4 / NOL6/Upt22 / Nrap protein PAP/OAS1-like domain 5 / Nrap protein domain 1 / Nrap protein domain 3 / Nrap protein domain 6 / Nrap protein domain 1 / Nrap protein, domain 2 ...Ribosomal RNA assembly KRR1 / rRNA-processing protein Fcf1, PIN domain / Nrap protein nucleotidyltransferase domain 4 / NOL6/Upt22 / Nrap protein PAP/OAS1-like domain 5 / Nrap protein domain 1 / Nrap protein domain 3 / Nrap protein domain 6 / Nrap protein domain 1 / Nrap protein, domain 2 / Nrap protein PAP/OAS-like domain / Nrap protein, domain 3 / Nrap protein, domain 6 / Nrap protein, domain 4 / Nrap protein, domain 5 / Rrp7 RRM-like N-terminal domain / Rrp7, RRM-like N-terminal domain / Ribosomal RNA-processing protein 7 / rRNA-processing protein Fcf1/Utp23 / Fcf1 / Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain / Ribosomal RNA-processing protein 7, C-terminal domain / NOP5NT (NUC127) domain / NOP5, N-terminal / RNA 3'-terminal phosphate cyclase signature. / RNA 3'-terminal phosphate cyclase-like, conserved site / Ribosome biogenesis protein Bms1, N-terminal / Small-subunit processome, Utp13 / Krr1, KH1 domain / Utp13 specific WD40 associated domain / Krr1 KH1 domain / Periodic tryptophan protein 2 / BP28, C-terminal domain / BP28CT (NUC211) domain / U3 small nucleolar RNA-associated protein 10, N-terminal / U3 small nucleolar RNA-associated protein 10 / U3 small nucleolar RNA-associated protein 10 / BP28CT (NUC211) domain / Mpp10 protein / U3 small nucleolar ribonucleoprotein complex, subunit Mpp10 / Small-subunit processome, Utp12 / Dip2/Utp12 Family / Ribosomal RNA-processing protein Rrp9-like / RNA 3'-terminal phosphate cyclase type 2 / Utp21 specific WD40 associated putative domain / Small-subunit processome, Utp21 / EMG1/NEP1 methyltransferase / Ribosomal biogenesis, methyltransferase, EMG1/NEP1 / Pre-rRNA-processing protein PNO1-like / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase domain / RNA 3'-terminal phosphate cyclase domain superfamily / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase, insert domain superfamily / RNA 3'-terminal phosphate cyclase (RTC), insert domain / U3 snoRNP protein/Ribosome production factor 1 / Fibrillarin / Fibrillarin / Fibrillarin, conserved site / Fibrillarin signature. / Fibrillarin / Protein of unknown function (DUF663) / Bms1-type guanine nucleotide-binding (G) domain profile. / AARP2CN / AARP2CN (NUC121) domain / Ribosome biogenesis protein Bms1/Tsr1 / 40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal / Bms1/Tsr1-type G domain / Ribosome biogenesis protein BMS1/TSR1, C-terminal / AARP2CN (NUC121) domain / Brix domain / Brix / Brix domain / Brix domain profile. / Large family of predicted nucleotide-binding domains / H/ACA ribonucleoprotein complex, subunit Nhp2, eukaryote / NOSIC (NUC001) domain / NOSIC / Nop domain superfamily / Nop domain / Nop, C-terminal domain / snoRNA binding domain, fibrillarin / Nop domain profile. / HEAT repeat profile. / HEAT, type 2 / PIN domain / Helix hairpin bin domain superfamily / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / K Homology domain, type 1 superfamily / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / Quinoprotein alcohol dehydrogenase-like superfamily / PIN-like domain superfamily / Ribosomal protein S30 / Ribosomal protein S30 / 40S ribosomal protein S4 C-terminus / 40S ribosomal protein S4, C-terminal domain
Similarity search - Domain/homology
13 kDa ribonucleoprotein-associated protein / U3 small nucleolar RNA-associated protein 18 / U3 small nucleolar RNA-associated protein 10 / U3 small nucleolar RNA-associated protein MPP10 / U3 small nucleolar RNA-associated protein 22 / U3 small nucleolar ribonucleoprotein protein IMP4 / rRNA-processing protein FCF1 / U3 small nucleolar RNA-associated protein 13 / U3 small nucleolar RNA-associated protein 21 / Ribosomal RNA small subunit methyltransferase NEP1 ...13 kDa ribonucleoprotein-associated protein / U3 small nucleolar RNA-associated protein 18 / U3 small nucleolar RNA-associated protein 10 / U3 small nucleolar RNA-associated protein MPP10 / U3 small nucleolar RNA-associated protein 22 / U3 small nucleolar ribonucleoprotein protein IMP4 / rRNA-processing protein FCF1 / U3 small nucleolar RNA-associated protein 13 / U3 small nucleolar RNA-associated protein 21 / Ribosomal RNA small subunit methyltransferase NEP1 / Ribosomal RNA-processing protein 9 / RNA 3'-terminal phosphate cyclase-like protein / Ribosome biogenesis protein BMS1 / U3 small nucleolar RNA-associated protein 12 / Nucleolar protein 56 / Nucleolar protein 58 / 40S ribosomal protein S28-A / Ribosome biogenesis protein UTP30 / 40S ribosomal protein S1-A / 40S ribosomal protein S27-A / 40S ribosomal protein S4-A / 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 S24-A / 40S ribosomal protein S30-A / 40S ribosomal protein S8-A / U3 small nucleolar ribonucleoprotein protein IMP3 / 40S ribosomal protein S11-A / 40S ribosomal protein S16-A / rRNA 2'-O-methyltransferase fibrillarin / Ribosomal RNA-processing protein 7 / KRR1 small subunit processome component / Periodic tryptophan protein 2 / 40S ribosomal protein S5 / 40S ribosomal protein S7-A / Pre-rRNA-processing protein PNO1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker's yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsYe K / Zhu X / Sun Q
CitationJournal: Elife / Year: 2017
Title: Molecular architecture of the 90S small subunit pre-ribosome.
Authors: Qi Sun / Xing Zhu / Jia Qi / Weidong An / Pengfei Lan / Dan Tan / Rongchang Chen / Bing Wang / Sanduo Zheng / Cheng Zhang / Xining Chen / Wei Zhang / Jing Chen / Meng-Qiu Dong / Keqiong Ye /
Abstract: Eukaryotic small ribosomal subunits are first assembled into 90S pre-ribosomes. The complete 90S is a gigantic complex with a molecular mass of approximately five megadaltons. Here, we report the ...Eukaryotic small ribosomal subunits are first assembled into 90S pre-ribosomes. The complete 90S is a gigantic complex with a molecular mass of approximately five megadaltons. Here, we report the nearly complete architecture of 90S determined from three cryo-electron microscopy single particle reconstructions at 4.5 to 8.7 angstrom resolution. The majority of the density maps were modeled and assigned to specific RNA and protein components. The nascent ribosome is assembled into isolated native-like substructures that are stabilized by abundant assembly factors. The 5' external transcribed spacer and U3 snoRNA nucleate a large subcomplex that scaffolds the nascent ribosome. U3 binds four sites of pre-rRNA, including a novel site on helix 27 but not the 3' side of the central pseudoknot, and crucially organizes the 90S structure. The 90S model provides significant insight into the principle of small subunit assembly and the function of assembly factors.
History
DepositionJan 13, 2017-
Header (metadata) releaseMar 29, 2017-
Map releaseMar 29, 2017-
UpdateMay 17, 2017-
Current statusMay 17, 2017Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.09
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  • Surface view colored by radius
  • Surface level: 0.09
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  • Surface view with fitted model
  • Atomic models: PDB-5wyk
  • Surface level: 0.09
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  • Surface view with fitted model
  • Atomic models: PDB-5ydt
  • Surface level: 0.09
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5ydt
  • 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_6696.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.76 Å/pix.
x 400 pix.
= 704. Å
1.76 Å/pix.
x 400 pix.
= 704. Å
1.76 Å/pix.
x 400 pix.
= 704. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.76 Å
Density
Contour LevelBy AUTHOR: 0.09 / Movie #1: 0.09
Minimum - Maximum-0.266547 - 0.55166775
Average (Standard dev.)0.00023664889 (±0.019919828)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 704.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.761.761.76
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z704.000704.000704.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.2670.5520.000

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Supplemental data

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Sample components

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Entire 90S small subunit pre-ribosome (Mtr4-depleted, Enp1-TAP)

EntireName: 90S small subunit pre-ribosome (Mtr4-depleted, Enp1-TAP)
Number of Components: 56

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Component #1: protein, 90S small subunit pre-ribosome (Mtr4-depleted, Enp1-TAP)

ProteinName: 90S small subunit pre-ribosome (Mtr4-depleted, Enp1-TAP)
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #2: nucleic-acid, U3 RNA

nucleic acidName: U3 RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: GUCGACGUAC UUCAUAGGAU CAUUUCUAUA GGAAUCGUCA CUCUUUGACU CUUCAAAAGA GCCACUGAAU CCAACUUGGU UGAUGAGUCC CAUAACCUUU GUACCCCAGA GUGAGAAACC GAAAUUGAAU CUAAAUUAGC UUGGUCCGCA AUCCUUAGCG GUUCGGCCAU ...Sequence:
GUCGACGUAC UUCAUAGGAU CAUUUCUAUA GGAAUCGUCA CUCUUUGACU CUUCAAAAGA GCCACUGAAU CCAACUUGGU UGAUGAGUCC CAUAACCUUU GUACCCCAGA GUGAGAAACC GAAAUUGAAU CUAAAUUAGC UUGGUCCGCA AUCCUUAGCG GUUCGGCCAU CUAUAAUUUU GAAUAAAAAU UUUGCUUUGC CGUUGCAUUU GUAGUUUUUU CCUUUGGAAG UAAUUACAAU AUUUUAUGGC GCGAUGAUCU UGACCCAUCC UAUGUACUUC UUUUUUGAAG GGAUAGGGCU CUAUGGGUGG GUACAAAUGG CAGUCUGACA AGU
MassTheoretical: 106.503258 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #3: 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 #4: 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 #5: 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 #6: 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 #7: 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 #8: 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: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #9: protein, Utp4

ProteinName: Utp4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 66.059172 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #10: protein, Utp5

ProteinName: Utp5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 54.740609 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #11: protein, Utp8

ProteinName: Utp8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 60.69775 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #12: protein, Utp9

ProteinName: Utp9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 48.953438 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 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 #14: protein, Utp15

ProteinName: Utp15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 43.676871 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #15: protein, Utp17

ProteinName: Utp17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 76.271414 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #16: 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 #17: 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 #18: 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 #19: 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 #20: 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 #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, 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 #23: 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 #24: 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 #25: protein, Enp2

ProteinName: Enp2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 60.187137 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #26: 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 #27: 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 #28: 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 #29: protein, Mpp10,U3 small nucleolar RNA-associated protein MPP10

ProteinName: Mpp10,U3 small nucleolar RNA-associated protein MPP10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 54.936984 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #30: 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 #31: 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 #32: protein, Sof1

ProteinName: Sof1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 41.634328 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #33: nucleic-acid, 18S ribosomal RNA

nucleic acidName: 18S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: UAUCUGGUUG AUCCUGCCAG UAGUCAUAUG CUUGUCUCAA AGAUUAAGCC AUGCAUGUCU AAGUAUAAGC AAUUUAUACA GUGAAACUGC GAAUGGCUCA UUAAAUCAGU UAUCGUUUAU UUGAUAGUUC CUUUACUACA UGGUAUAACU GUGGUAAUUC UAGAGCUAAU ...Sequence:
UAUCUGGUUG AUCCUGCCAG UAGUCAUAUG CUUGUCUCAA AGAUUAAGCC AUGCAUGUCU AAGUAUAAGC AAUUUAUACA GUGAAACUGC GAAUGGCUCA UUAAAUCAGU UAUCGUUUAU UUGAUAGUUC CUUUACUACA UGGUAUAACU GUGGUAAUUC UAGAGCUAAU ACAUGCUUAA AAUCUCGACC CUUUGGAAGA GAUGUAUUUA UUAGAUAAAA AAUCAAUGUC UUCGGACUCU UUGAUGAUUC AUAAUAACUU UUCGAAUCGC AUGGCCUUGU GCUGGCGAUG GUUCAUUCAA AUUUCUGCCC UAUCAACUUU CGAUGGUAGG AUAGUGGCCU ACCAUGGUUU CAACGGGUAA CGGGGAAUAA GGGUUCGAUU CCGGAGAGGG AGCCUGAGAA ACGGCUACCA CAUCCAAGGA AGGCAGCAGG CGCGCAAAUU ACCCAAUCCU AAUUCAGGGA GGUAGUGACA AUAAAUAACG AUACAGGGCC CAUUCGGGUC UUGUAAUUGG AAUGAGUACA AUGUAAAUAC CUUAACGAGG AACAAUUGGA GGGCAAGUCU GGUGCCAGCA GCCGCGGUAA UUCCAGCUCC AAUAGCGUAU AUUAAAGUUG UUGCAGUUAA AAAGCUCGUA GUUGAACUUU GGGCCCGGUU GGCCGGUCCG AUUUUUUCGU GUACUGGAUU UCCAACGGGG CCUUUCCUUC UGGCUAACCU UGAGUCCUUG UGGCUCUUGG CGAACCAGGA CUUUUACUUU GAAAAAAUUA GAGUGUUCAA AGCAGGCGUA UUGCUCGAAU AUAUUAGCAU GGAAUAAUAG AAUAGGACGU UUGGUUCUAU UUUGUUGGUU UCUAGGACCA UCGUAAUGAU UAAUAGGGAC GGUCGGGGGC AUCAGUAUUC AAUUGUCAGA GGUGAAAUUC UUGGAUUUAU UGAAGACUAA CUACUGCGAA AGCAUUUGCC AAGGACGUUU UCAUUAAUCA AGAACGAAAG UUAGGGGAUC GAAGAUGAUC AGAUACCGUC GUAGUCUUAA CCAUAAACUA UGCCGACUAG GGAUCGGGUG GUGUUUUUUU AAUGACCCAC UCGGCACCUU ACGAGAAAUC AAAGUCUUUG GGUUCUGGGG GGAGUAUGGU CGCAAGGCUG AAACUUAAAG GAAUUGACGG AAGGGCACCA CCAGGAGUGG AGCCUGCGGC UUAAUUUGAC UCAACACGGG GAAACUCACC AGGUCCAGAC ACAAUAAGGA UUGACAGAUU GAGAGCUCUU UCUUGAUUUU GUGGGUGGUG GUGCAUGGCC GUUCUUAGUU GGUGGAGUGA UUUGUCUGCU UAAUUGCGAU AACGAACGAG ACCUUAACCU ACUAAAUAGU GGUGCUAGCA UUUGCUGGUU AUCCACUUCU UAGAGGGACU AUCGGUUUCA AGCCGAUGGA AGUUUGAGGC AAUAACAGGU CUGUGAUGCC CUUAGACGUU CUGGGCCGCA CGCGCGCUAC ACUGACGGAG CCAGCGAGUC UAACCUUGGC CGAGAGGUCU UGGUAAUCUU GUGAAACUCC GUCGUGCUGG GGAUAGAGCA UUGUAAUUAU UGCUCUUCAA CGAGGAAUUC CUAGUAAGCG CAAGUCAUCA GCUUGCGUUG AUUACGUCCC UGCCCUUUGU ACACACCGCC CGUCGCUAGU ACCGAUUGAA UGGCUUAGUG AGGCCUCAGG AUCUGCUUAG AGAAGGGGGC AACUCCAUCU CAGAGCGGAG AAUUUGGACA AACUUGGUCA UUUAGAGGAA CUAAAAGUCG UAACAAGGUU UCCGUAGGUG AACCUGCGGA AGGAUCAUUA AAGAAAUUUA AU
MassTheoretical: 583.636562 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #34: 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

+
Component #35: protein, 40S ribosomal protein S4-A

ProteinName: 40S ribosomal protein S4-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.46933 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #36: protein, 40S ribosomal protein S5

ProteinName: 40S ribosomal protein S5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.0726 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #37: 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

+
Component #38: protein, 40S ribosomal protein S8-A

ProteinName: 40S ribosomal protein S8-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.537803 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #39: 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

+
Component #40: protein, 40S ribosomal protein S11-A

ProteinName: 40S ribosomal protein S11-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.785934 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #41: 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

+
Component #42: 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 #43: 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 #44: 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 #45: 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 #46: protein, 40S ribosomal protein S24-A

ProteinName: 40S ribosomal protein S24-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.362848 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #47: 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 #48: 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 #49: protein, 40S ribosomal protein S30-A

ProteinName: 40S ribosomal protein S30-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.137541 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #50: protein, Utp7

ProteinName: Utp7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 47.166211 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #51: protein, Utp11

ProteinName: Utp11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.294152 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #52: 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

+
Component #53: 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

+
Component #54: protein, Helical domain protein

ProteinName: Helical domain protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 137.462422 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #55: protein, Helical domain protein

ProteinName: Helical domain protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 84.015695 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

+
Component #56: protein, Unassigned helices

ProteinName: Unassigned helices / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 87.930383 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Experimental details

-
Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: ETHANE / Temperature: 277.15 K / Humidity: 100 % / Details: blot for 2 seconds before plunging.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 40 e/Å2 / Illumination Mode: FLOOD BEAM
LensMagnification: 45000.0 X (nominal), 79545.0 X (calibrated) / Cs: 2.7 mm / Imaging Mode: BRIGHT FIELD / Defocus: 1500.0 - 3500.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: OTHER

-
Image acquisition

Image acquisitionNumber of Digital Images: 1102

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Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 73543 / Details: detector is Falcon III
3D reconstructionSoftware: Relion / Resolution: 4.5 Å / Resolution Method: FSC 0.143 CUT-OFF / Euler angles: using Relion default parameters
FSC plot (resolution estimation)

-
Atomic model buiding

Output model

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