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- EMDB-8859: The complete structure of the small subunit processome -

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Basic information

Entry
Database: EMDB / ID: 8859
TitleThe complete structure of the small subunit processome
Map datasmall subunit processome, overall map 1
SampleSmall subunit processome:
(nucleic-acidNucleic acid) x 3 / rpS18_uS13 / rpS4_eS4 / rpS5_uS7 / rpS6_eS6 / rpS7_eS7 / rpS8_eS8 / rpS9_uS4 / rpS16_uS9 / rpS11_uS17 ...(nucleic-acidNucleic acid) x 3 / rpS18_uS13 / rpS4_eS4 / rpS5_uS7 / rpS6_eS6 / rpS7_eS7 / rpS8_eS8 / rpS9_uS4 / rpS16_uS9 / rpS11_uS17 / rpS22_uS8 / rpS24_eS24 / rpS28_eS28 / Utp17 / Utp8 / Utp15 / Utp9 / Utp5 / Utp10 / Utp4 / Utp1 / Utp6 / Utp12 / Utp13 / Utp18 / Utp21 / Sof1 / Enp2 / Utp7 / Kre33 / Imp3 / Mpp10 / Sas10 / Lcp5 / Bud21 / Faf1 / rpS13_uS15 / rpS14_uS11 / Utp22 / Rrp7 / Rrp5 / Krr1 / Nop56 / Nop58 / Nop1 / Snu13 / Rrp9 / Rcl1 / Bms1 / Emg1 / Utp24 / Imp4 / Utp30 / Pno1 / Utp20 / Fcf2 / rpS23_uS12 / Utp14 / Nop14 / Noc4 / Rrt14 / Unassigned peptides / Utp11 / Enp1 / ligand
Function / homologyP-loop containing nucleoside triphosphate hydrolase / Ribosomal protein S17, archaeal/eukaryotic / S-adenosyl-L-methionine-dependent methyltransferase / PIN-like domain superfamily / Alpha/beta knot methyltransferases / tRNA (guanine-N1-)-methyltransferase, N-terminal / Helix hairpin bin domain superfamily / Ribosomal protein S28e conserved site / Ribosomal protein L1/ribosomal biogenesis protein / Possible tRNA binding domain ...P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein S17, archaeal/eukaryotic / S-adenosyl-L-methionine-dependent methyltransferase / PIN-like domain superfamily / Alpha/beta knot methyltransferases / tRNA (guanine-N1-)-methyltransferase, N-terminal / Helix hairpin bin domain superfamily / Ribosomal protein S28e conserved site / Ribosomal protein L1/ribosomal biogenesis protein / Possible tRNA binding domain / Bms1/Tsr1-type G domain / 30s ribosomal protein S13, C-terminal / Nucleolar complex protein 4 / Periodic tryptophan protein 2 / Anaphase-promoting complex subunit 4, WD40 domain / Ribosomal RNA-processing protein 7 / Ribosomal RNA assembly KRR1 / Ribosomal protein S7 domain / 50S ribosomal protein L30e-like / Regulator of rDNA transcription 14 / Ribosomal protein L1-like / Nrap protein, domain 6 / Ribosomal protein S11 superfamily / Ribosomal protein S7 domain superfamily / K Homology domain, type 1 superfamily / RNA 3'-terminal phosphate cyclase, insert domain superfamily / WD40-repeat-containing domain superfamily / Nop domain superfamily / Ribosomal protein S8 superfamily / Nrap protein, domain 5 / 40S ribosomal protein S4, C-terminal domain / Nrap protein, domain 4 / Nrap protein, domain 3 / Nrap protein, domain 2 / Nrap protein domain 1 / RNA cytidine acetyltransferase NAT10 / TmcA/NAT10/Kre33 / 40S ribosomal protein S11, N-terminal / RNA 3'-terminal phosphate cyclase domain / Ribosomal protein S15P / RNA 3'-terminal phosphate cyclase domain superfamily / Fcf2 pre-rRNA processing / Ribosomal S11, conserved site / Ribosomal S24e conserved site / Ribosomal protein S4, conserved site / WD40-repeat-containing domain / RNA 3'-terminal phosphate cyclase type 2 / Armadillo-type fold / WD40/YVTN repeat-like-containing domain superfamily / Ribosomal protein L2, domain 2 / Ribosomal protein S13, conserved site / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S6, eukaryotic / U3 small nucleolar RNA-associated protein 6 / Small-subunit processome, Utp13 / Ribosomal protein S4e, central region / Ribosomal protein S4e, N-terminal / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S6e, conserved site / RNA-binding domain, S1 / Ribosomal protein S9, conserved site / Ribosomal protein S4/S9 / Ribosomal protein S8e/ribosomal biogenesis NSA2 / U3 small nucleolar RNA-associated protein 10 / HEAT, type 2 / Fibrillarin, conserved site / RNA 3'-terminal phosphate cyclase-like, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S8e, conserved site / G-protein beta WD-40 repeat / Ribosomal protein S17, conserved site / WD40 repeat, conserved site / U3 small nucleolar RNA-associated protein 15, C-terminal / Sas10 C-terminal domain / U3 small nucleolar RNA-associated protein 8 / Ribosomal protein L7Ae/L8/Nhp2 family / RNA-binding S4 domain superfamily / rRNA-processing protein Fcf1, PIN domain / tRNA(Met) cytidine acetyltransferase TmcA, N-terminal / NUC153 domain / UTP15 C terminal / Sas10 C-terminal domain / Fcf2 pre-rRNA processing / U3 small nucleolar RNA-associated protein 6 / Utp13 specific WD40 associated domain / Domain of unknown function (DUF1726) / U3 snoRNA associated / NOP5NT (NUC127) domain / U3 small nucleolar RNA-associated protein 10 / BING4CT (NUC141) domain / BP28CT (NUC211) domain / AARP2CN (NUC121) domain / RS4NT (NUC023) domain / Ribosomal S13/S15 N-terminal domain / Bystin / RNA 3'-terminal phosphate cyclase (RTC), insert domain / Utp8 family / Anaphase-promoting complex subunit 4 WD40 domain
Function and homology information
SourceSaccharomyces cerevisiae BY4741 (yeast)
Methodsingle particle reconstruction / cryo EM / 3.8 Å resolution
AuthorsBarandun J / Chaker-Margot M
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: The complete structure of the small-subunit processome.
Authors: Jonas Barandun / Malik Chaker-Margot / Mirjam Hunziker / Kelly R Molloy / Brian T Chait / Sebastian Klinge
Validation ReportPDB-ID: 5wlc

SummaryFull reportAbout validation report
DateDeposition: Jul 26, 2017 / Header (metadata) release: Sep 13, 2017 / Map release: Sep 27, 2017 / Last update: Nov 22, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.023
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.023
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5wlc
  • Surface level: 0.023
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8859.map.gz (map file in CCP4 format, 256001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
400 pix
1.3 Å/pix.
= 520. Å
400 pix
1.3 Å/pix.
= 520. Å
400 pix
1.3 Å/pix.
= 520. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density
Contour Level:0.023 (by author), 0.023 (movie #1):
Minimum - Maximum-0.10548593 - 0.16638078
Average (Standard dev.)0.00023483255 (0.005812679)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions400400400
Origin000
Limit399399399
Spacing400400400
CellA=B=C: 520 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z520.000520.000520.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.1050.1660.000

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Supplemental data

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Sample components

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Entire Small subunit processome

EntireName: Small subunit processome / Number of components: 68

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Component #1: protein, Small subunit processome

ProteinName: Small subunit processome / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast)

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Component #2: nucleic-acid, 5' ETS

Nucleic-acidName: 5' ETS / Class: RNA / Structure: OTHER / Synthetic: No
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 BY4741 (yeast) / Strain: BY4741

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Component #3: nucleic-acid, 18S pre-rRNA

Nucleic-acidName: 18S pre-rRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AGAUAGUUAU CUGGUUGAUC CUGCCAGUAG UCAUAUGCUU GUCUCAAAGA UUAAGCCAUG CAUGUCUAAG UAUAAGCAAU UUAUACAGUG AAACUGCGAA UGGCUCAUUA AAUCAGUUAU CGUUUAUUUG AUAGUUCCUU UACUACAUGG UAUAACUGUG GUAAUUCUAG AGCUAAUACA UGCUUAAAAU CUCGACCCUU UGGAAGAGAU GUAUUUAUUA GAUAAAAAAU CAAUGUCUUC GGACUCUUUG AUGAUUCAUA AUAACUUUUC GAAUCGCAUG GCCUUGUGCU GGCGAUGGUU CAUUCAAAUU UCUGCCCUAU CAACUUUCGA UGGUAGGAUA GUGGCCUACC AUGGUUUCAA CGGGUAACGG GGAAUAAGGG UUCGAUUCCG GAGAGGGAGC CUGAGAAACG GCUACCACAU CCAAGGAAGG CAGCAGGCGC GCAAAUUACC CAAUCCUAAU UCAGGGAGGU AGUGACAAUA AAUAACGAUA CAGGGCCCAU UCGGGUCUUG UAAUUGGAAU GAGUACAAUG UAAAUACCUU AACGAGGAAC AAUUGGAGGG CAAGUCUGGU GCCAGCAGCC GCGGUAAUUC CAGCUCCAAU AGCGUAUAUU AAAGUUGUUG CAGUUAAAAA GCUCGUAGUU GAACUUUGGG CCCGGUUGGC CGGUCCGAUU UUUUCGUGUA CUGGAUUUCC AACGGGGCCU UUCCUUCUGG CUAACCUUGA GUCCUUGUGG CUCUUGGCGA ACCAGGACUU UUACUUUGAA AAAAUUAGAG UGUUCAAAGC AGGCGUAUUG CUCGAAUAUA UUAGCAUGGA AUAAUAGAAU AGGACGUUUG GUUCUAUUUU GUUGGUUUCU AGGACCAUCG UAAUGAUUAA UAGGGACGGU CGGGGGCAUC AGUAUUCAAU UGUCAGAGGU GAAAUUCUUG GAUUUAUUGA AGACUAACUA CUGCGAAAGC AUUUGCCAAG GACGUUUUCA UUAAUCAAGA ACGAAAGUUA GGGGAUCGAA GAUGAUCAGA UACCGUCGUA GUCUUAACCA UAAACUAUGC CGACUAGGGA UCGGGUGGUG UUUUUUUAAU GACCCACUCG GCACCUUACG AGAAAUCAAA GUCUUUGGGU UCUGGGGGGA GUAUGGUCGC AAGGCUGAAA CUUAAAGGAA UUGACGGAAG GGCACCACCA GGAGUGGAGC CUGCGGCUUA AUUUGACUCA ACACGGGGAA ACUCACCAGG UCCAGACACA AUAAGGAUUG ACAGAUUGAG AGCUCUUUCU UGAUUUUGUG GGUGGUGGUG CAUGGCCGUU CUUAGUUGGU GGAGUGAUUU GUCUGCUUAA UUGCGAUAAC GAACGAGACC UUAACCUACU AAAUAGUGGU GCUAGCAUUU GCUGGUUAUC CACUUCUUAG AGGGACUAUC GGUUUCAAGC CGAUGGAAGU UUGAGGCAAU AACAGGUCUG UGAUGCCCUU AGACGUUCUG GGCCGCACGC GCGCUACACU GACGGAGCCA GCGAGUCUAA CCUUGGCCGA GAGGUCUUGG UAAUCUUGUG AAACUCCGUC GUGCUGGGGA UAGAGCAUUG UAAUUAUUGC UCUUCAACGA GGAAUUCCUA GUAAGCGCAA GUCAUCAGCU UGCGUUGAUU ACGUCCCUGC CCUUUGUACA CACCGCCCGU CGCUAGUACC GAUUGAAUGG CUUAGUGAGG CCUCAGGAUC UGCUUAGAGA AGGGGGCAAC UCCAUCUCAG AGCGGAGAAU UUGGACAAAC UUGGUCAUUU AGAGGAACUA AAAGUCGUAA CAAGGUUUCC GUAGGUGAAC CUGCGGAAGG AUCAUUA
MassTheoretical: 582.052438 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #4: 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 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: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #5: protein, rpS18_uS13

ProteinName: rpS18_uS13 / Recombinant expression: No
MassTheoretical: 16.773332 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #6: protein, rpS4_eS4

ProteinName: rpS4_eS4 / Recombinant expression: No
MassTheoretical: 29.46933 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #7: protein, rpS5_uS7

ProteinName: rpS5_uS7 / Recombinant expression: No
MassTheoretical: 25.0726 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #8: protein, rpS6_eS6

ProteinName: rpS6_eS6 / Recombinant expression: No
MassTheoretical: 27.054486 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #9: protein, rpS7_eS7

ProteinName: rpS7_eS7 / Recombinant expression: No
MassTheoretical: 21.658209 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #10: protein, rpS8_eS8

ProteinName: rpS8_eS8 / Recombinant expression: No
MassTheoretical: 22.537803 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #11: protein, rpS9_uS4

ProteinName: rpS9_uS4 / Recombinant expression: No
MassTheoretical: 22.487893 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #12: protein, rpS16_uS9

ProteinName: rpS16_uS9 / Recombinant expression: No
MassTheoretical: 15.87749 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #13: protein, rpS11_uS17

ProteinName: rpS11_uS17 / Recombinant expression: No
MassTheoretical: 17.785934 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #14: protein, rpS22_uS8

ProteinName: rpS22_uS8 / Recombinant expression: No
MassTheoretical: 14.650062 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #15: protein, rpS24_eS24

ProteinName: rpS24_eS24 / Recombinant expression: No
MassTheoretical: 15.362848 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #16: protein, rpS28_eS28

ProteinName: rpS28_eS28 / Recombinant expression: No
MassTheoretical: 7.605847 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #17: protein, Utp17

ProteinName: Utp17 / Recombinant expression: No
MassTheoretical: 100.960445 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #18: protein, Utp8

ProteinName: Utp8 / Recombinant expression: No
MassTheoretical: 65.572977 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #19: protein, Utp15

ProteinName: Utp15 / Recombinant expression: No
MassTheoretical: 57.765289 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #20: protein, Utp9

ProteinName: Utp9 / Recombinant expression: No
MassTheoretical: 64.378512 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #21: protein, Utp5

ProteinName: Utp5 / Recombinant expression: No
MassTheoretical: 72.079445 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #22: protein, Utp10

ProteinName: Utp10 / Recombinant expression: No
MassTheoretical: 200.020719 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #23: protein, Utp4

ProteinName: Utp4 / Recombinant expression: No
MassTheoretical: 87.3165 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #24: protein, Utp1

ProteinName: Utp1 / Recombinant expression: No
MassTheoretical: 104.097039 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #25: protein, Utp6

ProteinName: Utp6 / Recombinant expression: No
MassTheoretical: 48.437402 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #26: protein, Utp12

ProteinName: Utp12 / Recombinant expression: No
MassTheoretical: 105.037648 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #27: protein, Utp13

ProteinName: Utp13 / Recombinant expression: No
MassTheoretical: 75.035867 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #28: protein, Utp18

ProteinName: Utp18 / Recombinant expression: No
MassTheoretical: 66.49425 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #29: protein, Utp21

ProteinName: Utp21 / Recombinant expression: No
MassTheoretical: 104.927844 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #30: protein, Sof1

ProteinName: Sof1 / Recombinant expression: No
MassTheoretical: 56.888918 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #31: protein, Enp2

ProteinName: Enp2 / Recombinant expression: No
MassTheoretical: 81.864172 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #32: protein, Utp7

ProteinName: Utp7 / Recombinant expression: No
MassTheoretical: 62.41857 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #33: protein, Kre33

ProteinName: Kre33 / Recombinant expression: No
MassTheoretical: 95.337062 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #34: protein, Imp3

ProteinName: Imp3 / Recombinant expression: No
MassTheoretical: 21.928529 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #35: protein, Mpp10

ProteinName: Mpp10 / Recombinant expression: No
MassTheoretical: 67.042492 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #36: protein, Sas10

ProteinName: Sas10 / Recombinant expression: No
MassTheoretical: 69.705703 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #37: protein, Lcp5

ProteinName: Lcp5 / Recombinant expression: No
MassTheoretical: 40.864391 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #38: protein, Bud21

ProteinName: Bud21 / Recombinant expression: No
MassTheoretical: 23.835627 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #39: protein, Faf1

ProteinName: Faf1 / Recombinant expression: No
MassTheoretical: 38.173699 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #40: protein, rpS13_uS15

ProteinName: rpS13_uS15 / Recombinant expression: No
MassTheoretical: 17.059945 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #41: protein, rpS14_uS11

ProteinName: rpS14_uS11 / Recombinant expression: No
MassTheoretical: 14.562655 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #42: protein, Utp22

ProteinName: Utp22 / Recombinant expression: No
MassTheoretical: 140.660141 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #43: protein, Rrp7

ProteinName: Rrp7 / Recombinant expression: No
MassTheoretical: 34.526441 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #44: protein, Rrp5

ProteinName: Rrp5 / Recombinant expression: No
MassTheoretical: 193.411422 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #45: protein, Krr1

ProteinName: Krr1 / Recombinant expression: No
MassTheoretical: 37.226254 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #46: protein, Nop56

ProteinName: Nop56 / Recombinant expression: No
MassTheoretical: 56.394863 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #47: protein, Nop58

ProteinName: Nop58 / Recombinant expression: No
MassTheoretical: 53.81452 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #48: protein, Nop1

ProteinName: Nop1 / Recombinant expression: No
MassTheoretical: 34.525418 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #49: protein, Snu13

ProteinName: Snu13 / Recombinant expression: No
MassTheoretical: 13.582855 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #50: protein, Rrp9

ProteinName: Rrp9 / Recombinant expression: No
MassTheoretical: 65.146969 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #51: protein, Rcl1

ProteinName: Rcl1 / Recombinant expression: No
MassTheoretical: 40.220559 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #52: protein, Bms1

ProteinName: Bms1 / Recombinant expression: No
MassTheoretical: 135.152938 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #53: protein, Emg1

ProteinName: Emg1 / Recombinant expression: No
MassTheoretical: 27.936461 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #54: protein, Utp24

ProteinName: Utp24 / Recombinant expression: No
MassTheoretical: 21.650729 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #55: protein, Imp4

ProteinName: Imp4 / Recombinant expression: No
MassTheoretical: 33.536168 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #56: protein, Utp30

ProteinName: Utp30 / Recombinant expression: No
MassTheoretical: 31.668939 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #57: protein, Pno1

ProteinName: Pno1 / Recombinant expression: No
MassTheoretical: 30.380623 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #58: protein, Utp20

ProteinName: Utp20 / Recombinant expression: No
MassTheoretical: 83.59018 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #59: protein, Fcf2

ProteinName: Fcf2 / Recombinant expression: No
MassTheoretical: 25.68924 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #60: protein, rpS23_uS12

ProteinName: rpS23_uS12 / Recombinant expression: No
MassTheoretical: 16.073896 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

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Component #61: protein, Utp14

ProteinName: Utp14 / Recombinant expression: No
MassTheoretical: 101.101461 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

+
Component #62: protein, Nop14

ProteinName: Nop14 / Recombinant expression: No
MassTheoretical: 85.993961 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

+
Component #63: protein, Noc4

ProteinName: Noc4 / Recombinant expression: No
MassTheoretical: 58.369125 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

+
Component #64: protein, Rrt14

ProteinName: Rrt14 / Recombinant expression: No
MassTheoretical: 21.036877 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

+
Component #65: protein, Unassigned peptides

ProteinName: Unassigned peptides / Recombinant expression: No
MassTheoretical: 8.783818 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

+
Component #66: protein, Utp11

ProteinName: Utp11 / Recombinant expression: No
MassTheoretical: 29.806348 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

+
Component #67: protein, Enp1

ProteinName: Enp1 / Recombinant expression: No
MassTheoretical: 55.207422 kDa
SourceSpecies: Saccharomyces cerevisiae BY4741 (yeast) / Strain: BY4741

+
Component #68: 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 solutionSpecimen conc.: 0.15 mg/ml / pH: 7.7
Support film50 mA
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 295 K / Humidity: 100 %

-
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: 1.56 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 22500 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 600 - 2600 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 10029

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 284213
3D reconstructionSoftware: RELION / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Output model

+
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Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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