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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
SampleSmall subunit processome
SourceSaccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Map datasmall subunit processome, overall map 1
Methodsingle particle reconstruction, at 3.8 Å resolution
AuthorsBarandun J / Chaker-Margot M
CitationNat. Struct. Mol. Biol., 2017, 24, 944-953

Nat. Struct. Mol. Biol., 2017, 24, 944-953 Yorodumi Papers
The complete structure of the small-subunit processome.
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
3D viewer


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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 package.

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 / image: Saccharomyces cerevisiae

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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 / image: Saccharomyces cerevisiae
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 / image: Saccharomyces cerevisiae
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 / image: Saccharomyces cerevisiae
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 / image: Saccharomyces cerevisiae
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 / image: Saccharomyces cerevisiae
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 / image: Saccharomyces cerevisiae
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 / image: Saccharomyces cerevisiae
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 / image: Saccharomyces cerevisiae
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 / image: Saccharomyces cerevisiae
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 / image: Saccharomyces cerevisiae
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 / image: Saccharomyces cerevisiae
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 / image: Saccharomyces cerevisiae
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 / image: Saccharomyces cerevisiae
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 / image: Saccharomyces cerevisiae
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 / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #17: protein, Utp17

ProteinName: Utp17 / Recombinant expression: No
MassTheoretical: 100.960445 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #18: protein, Utp8

ProteinName: Utp8 / Recombinant expression: No
MassTheoretical: 65.572977 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #19: protein, Utp15

ProteinName: Utp15 / Recombinant expression: No
MassTheoretical: 57.765289 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #20: protein, Utp9

ProteinName: Utp9 / Recombinant expression: No
MassTheoretical: 64.378512 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #21: protein, Utp5

ProteinName: Utp5 / Recombinant expression: No
MassTheoretical: 72.079445 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #22: protein, Utp10

ProteinName: Utp10 / Recombinant expression: No
MassTheoretical: 200.020719 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #23: protein, Utp4

ProteinName: Utp4 / Recombinant expression: No
MassTheoretical: 87.3165 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #24: protein, Utp1

ProteinName: Utp1 / Recombinant expression: No
MassTheoretical: 104.097039 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #25: protein, Utp6

ProteinName: Utp6 / Recombinant expression: No
MassTheoretical: 48.437402 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #26: protein, Utp12

ProteinName: Utp12 / Recombinant expression: No
MassTheoretical: 105.037648 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #27: protein, Utp13

ProteinName: Utp13 / Recombinant expression: No
MassTheoretical: 75.035867 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #28: protein, Utp18

ProteinName: Utp18 / Recombinant expression: No
MassTheoretical: 66.49425 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #29: protein, Utp21

ProteinName: Utp21 / Recombinant expression: No
MassTheoretical: 104.927844 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #30: protein, Sof1

ProteinName: Sof1 / Recombinant expression: No
MassTheoretical: 56.888918 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #31: protein, Enp2

ProteinName: Enp2 / Recombinant expression: No
MassTheoretical: 81.864172 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #32: protein, Utp7

ProteinName: Utp7 / Recombinant expression: No
MassTheoretical: 62.41857 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #33: protein, Kre33

ProteinName: Kre33 / Recombinant expression: No
MassTheoretical: 95.337062 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #34: protein, Imp3

ProteinName: Imp3 / Recombinant expression: No
MassTheoretical: 21.928529 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #35: protein, Mpp10

ProteinName: Mpp10 / Recombinant expression: No
MassTheoretical: 67.042492 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #36: protein, Sas10

ProteinName: Sas10 / Recombinant expression: No
MassTheoretical: 69.705703 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #37: protein, Lcp5

ProteinName: Lcp5 / Recombinant expression: No
MassTheoretical: 40.864391 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #38: protein, Bud21

ProteinName: Bud21 / Recombinant expression: No
MassTheoretical: 23.835627 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #39: protein, Faf1

ProteinName: Faf1 / Recombinant expression: No
MassTheoretical: 38.173699 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
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 / image: Saccharomyces cerevisiae
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 / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #42: protein, Utp22

ProteinName: Utp22 / Recombinant expression: No
MassTheoretical: 140.660141 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #43: protein, Rrp7

ProteinName: Rrp7 / Recombinant expression: No
MassTheoretical: 34.526441 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #44: protein, Rrp5

ProteinName: Rrp5 / Recombinant expression: No
MassTheoretical: 193.411422 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #45: protein, Krr1

ProteinName: Krr1 / Recombinant expression: No
MassTheoretical: 37.226254 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #46: protein, Nop56

ProteinName: Nop56 / Recombinant expression: No
MassTheoretical: 56.394863 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #47: protein, Nop58

ProteinName: Nop58 / Recombinant expression: No
MassTheoretical: 53.81452 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #48: protein, Nop1

ProteinName: Nop1 / Recombinant expression: No
MassTheoretical: 34.525418 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #49: protein, Snu13

ProteinName: Snu13 / Recombinant expression: No
MassTheoretical: 13.582855 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #50: protein, Rrp9

ProteinName: Rrp9 / Recombinant expression: No
MassTheoretical: 65.146969 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #51: protein, Rcl1

ProteinName: Rcl1 / Recombinant expression: No
MassTheoretical: 40.220559 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #52: protein, Bms1

ProteinName: Bms1 / Recombinant expression: No
MassTheoretical: 135.152938 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #53: protein, Emg1

ProteinName: Emg1 / Recombinant expression: No
MassTheoretical: 27.936461 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #54: protein, Utp24

ProteinName: Utp24 / Recombinant expression: No
MassTheoretical: 21.650729 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #55: protein, Imp4

ProteinName: Imp4 / Recombinant expression: No
MassTheoretical: 33.536168 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #56: protein, Utp30

ProteinName: Utp30 / Recombinant expression: No
MassTheoretical: 31.668939 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #57: protein, Pno1

ProteinName: Pno1 / Recombinant expression: No
MassTheoretical: 30.380623 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #58: protein, Utp20

ProteinName: Utp20 / Recombinant expression: No
MassTheoretical: 83.59018 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #59: protein, Fcf2

ProteinName: Fcf2 / Recombinant expression: No
MassTheoretical: 25.68924 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
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 / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #61: protein, Utp14

ProteinName: Utp14 / Recombinant expression: No
MassTheoretical: 101.101461 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #62: protein, Nop14

ProteinName: Nop14 / Recombinant expression: No
MassTheoretical: 85.993961 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #63: protein, Noc4

ProteinName: Noc4 / Recombinant expression: No
MassTheoretical: 58.369125 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #64: protein, Rrt14

ProteinName: Rrt14 / Recombinant expression: No
MassTheoretical: 21.036877 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #65: protein, Unassigned peptides

ProteinName: Unassigned peptides / Recombinant expression: No
MassTheoretical: 8.783818 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #66: protein, Utp11

ProteinName: Utp11 / Recombinant expression: No
MassTheoretical: 29.806348 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #67: protein, Enp1

ProteinName: Enp1 / Recombinant expression: No
MassTheoretical: 55.207422 kDa
SourceSpecies: Saccharomyces cerevisiae by4741 / yeast / image: Saccharomyces cerevisiae
Strain: BY4741

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Component #68: ligand, ZINC ION

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

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Experimental details

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Sample preparation

Specimen stateparticle
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 %

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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: 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)

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Image acquisition

Image acquisitionNumber of digital images: 10029

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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 assessment)

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Atomic model buiding

Output model

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About Yorodumi

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News

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Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

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Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

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Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Read more

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

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