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- EMDB-6780: Small subunit of Toxoplasma gondii ribosome -

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Entry
Database: EMDB / ID: 6780
TitleSmall subunit of Toxoplasma gondii ribosome
SampleSmall subunit of Toxoplasma gondii ribosome
SourceToxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /
Map data
Methodsingle particle reconstruction, at 3.35 Å resolution
AuthorsLI Z / Guo Q
CitationCell Res., 2017, 27, 1275-1288

Cell Res., 2017, 27, 1275-1288 Yorodumi Papers
Cryo-EM structures of the 80S ribosomes from human parasites Trichomonas vaginalis and Toxoplasma gondii.
Zhifei Li / Qiang Guo / Lvqin Zheng / Yongsheng Ji / Yi-Ting Xie / De-Hua Lai / Zhao-Rong Lun / Xun Suo / Ning Gao

Validation ReportPDB-ID: 5xxu

SummaryFull reportAbout validation report
DateDeposition: Jul 5, 2017 / Header (metadata) release: Aug 30, 2017 / Map release: Aug 30, 2017 / Last update: Oct 18, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 0.03
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5xxu
  • Surface level: 0.03
  • Imaged by UCSF CHIMERA
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Supplemental images

Downloads & links

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Map

Fileemd_6780.map.gz (map file in CCP4 format, 131073 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
320 pix
1.32 Å/pix.
= 422.4 Å
320 pix
1.32 Å/pix.
= 422.4 Å
320 pix
1.32 Å/pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.32 Å
Density
Contour Level:0.03 (by author), 0.03 (movie #1):
Minimum - Maximum-0.11514145 - 0.20913129
Average (Standard dev.)0.000327257 (0.0049943044)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions320320320
Origin000
Limit319319319
Spacing320320320
CellA=B=C: 422.40002 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z422.400422.400422.400
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.1150.2090.000

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Supplemental data

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Mask #1

Fileemd_6780_msk_1.map ( map file in CCP4 format, 131073 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Space group number1

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Mask #1~

Fileemd_6780_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire Small subunit of Toxoplasma gondii ribosome

EntireName: Small subunit of Toxoplasma gondii ribosome / Number of components: 35

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Component #1: protein, Small subunit of Toxoplasma gondii ribosome

ProteinName: Small subunit of Toxoplasma gondii ribosome / Recombinant expression: No
SourceSpecies: Toxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /

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Component #2: nucleic-acid, 18S RNA

Nucleic-acidName: 18S RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AACCUGGUUG AUCCUGCCAG UAGUCAUAUG CUUGUCUUAA AGAUUAAGCC AUGCAUGUCU AAGUAUAAGC UUUUAUACGG CUAAACUGCG AAUGGCUCAU UAAAACAGUU AUAGUUUAUU UGAUGGUCUU UACUACAUGG AUAACCGUGG UAAUUCUAUG GCUAAUACCU GCGCACAUGC CUCUUCCCCU GGAAGGCAGU GUUUAUUAGA UACAGAACCA ACCCACCUUC CGGUGGUCCU CAGGUGAUUC AUAGUAACCG AACGGAUCGC GUUGACUUCG GUCUGCGACG GAUCAUUCAA GUUUCUGACC UAUCAGCUUU CGACGGUACU GUAAUGGACU ACCGUGGCAG UGACGGGUAA CGGGGAAUUA GGGUUCGAUU CCGGAGAGGG AGCCUGAGAA ACGGCUACCA CAUCUAAGGA AGGCAGCAGG CGCGCAAAUU ACCCAAUCCU GAUUCAGGGA GGUAGUGACA AGAAAUAACA ACACUGGAAA UUUCAUUUCU AGUGAUUGGA AUGAUAGGAA UCCAAACCCC UUUCAGAGUA ACAAUUGGAG GGCAAGUCUG GUGCCAGCAG CCGCGGUAAU UCCAGCUCCA AUAGCGUAUA UUAAAGUUGU UGCAGUUAAA AAGCUCGUAG UUGGAUUUCU GCUGGAAGGC CAGUCCGCCC UCAGGGGUGU GCACUUGGUG AAUUCUAGCA UCCUUCUGGA UUUCUCCACA CUUCAUUGUG UGGAGUUUUU UCCAGGACUU UUACUUUGAG AAAAUUAGAG UGUUUCAAGC AGGCUUGUCG CCUUGAAUAC UGCAGCAUGG AAUAAUAAGA UAGGAUUUCG GCCCUAUUUU GUUGGUUUCU AGGACUGAAG UAAUGAUUAA UAGGGACGGU UGGGGGCAUU CGUAUUUAAC UGUCAGAGGU GAAAUUCUUA GAUUUGUUAA AGACGAACUA CUGCGAAAGC AUUUGCCAAA GAUGUUUUCA UUAAUCAAGA ACGAAAGUUA GGGGCUCGAA GACGAUCAGA UACCGUCGUA GUCUUAACCA UAAACUAUGC CGACUAGAGA UAGGAAAACG UCAUGCUUGA CUUCUCCUGC ACCUUAUGAG AAACCAAAGU CUUUGGGUUC UGGGGGGAGU AUGGUCGCAA GGCUGAAACU UAAAGGAAUU GACGGAAGGG CACCACCAGG CGUGGAGCCU GCGGCUUAAU UUGACUCAAC ACGGGGAAAC UCACCAGGUC CAGACAUAGG AAGGAUUGAC AGAUUGAUAG CUCUUUCUUG AUUCUAUGGG UGGUGGUGCA UGGCCGUUCU UAGUUGGUGG AGUGAUUUGU CUGGUUAAUU CCGUUAACGA ACGAGACCUU AACCUGCUAA AUAGGAUCAG GAACUUCGUG UUCUUGUAUC ACUUCUUAGA GGGACUUUGC GUGUCUAACG CAAGGAAGUU UGAGGCAAUA ACAGGUCUGU GAUGCCCUUA GAUGUUCUGG GCUGCACGCG CGCUACACUG AUGCAUCCAA CGAGUUUAUA ACCUUGGCCG AUAGGUCUAG GUAAUCUUGU GAGUAUGCAU CGUGAUGGGG AUAGAUUAUU GCAAUUAUUA AUCUUCAACG AGGAAUGCCU AGUAGGCGCA AGUCAGCACG UUGCGCCGAU UACGUCCCUG CCCUUUGUAC ACACCGCCCG UCGCUCCUAC CGAUUGAGUG UUCCGGUGAA UUAUUCGGAC CGUUUUGUGG CGCGUUCGUG CCCGAAAUGG GAAGUUUUGU GAACCUUAAC ACUUAGAGGA AGGAGAAGUC GUAACAAGGU UUCCGUAGGU GAACCUGCGG AAGGAUCAUU C
MassTheoretical: 576.630812 kDa
SourceSpecies: Toxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /

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Component #3: protein, Ribosomal protein uS2

ProteinName: Ribosomal protein uS2 / Recombinant expression: No
MassTheoretical: 31.546902 kDa
SourceSpecies: Toxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /

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Component #4: protein, Ribosomal protein eS1

ProteinName: Ribosomal protein eS1 / Recombinant expression: No
MassTheoretical: 29.425625 kDa
SourceSpecies: Toxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /

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Component #5: protein, Ribosomal protein uS5

ProteinName: Ribosomal protein uS5 / Recombinant expression: No
MassTheoretical: 29.385004 kDa
SourceSpecies: Toxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /

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Component #6: protein, Ribosomal protein uS3

ProteinName: Ribosomal protein uS3 / Recombinant expression: No
MassTheoretical: 26.117539 kDa
SourceSpecies: Toxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /

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Component #7: protein, Ribosomal protein eS4

ProteinName: Ribosomal protein eS4 / Recombinant expression: No
MassTheoretical: 30.204713 kDa
SourceSpecies: Toxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /

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Component #8: protein, Ribosomal protein uS7

ProteinName: Ribosomal protein uS7 / Recombinant expression: No
MassTheoretical: 21.650238 kDa
SourceSpecies: Toxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /

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Component #9: protein, Ribosomal protein eS6

ProteinName: Ribosomal protein eS6 / Recombinant expression: No
MassTheoretical: 29.027504 kDa
SourceSpecies: Toxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /

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Component #10: protein, Ribosomal protein eS7

ProteinName: Ribosomal protein eS7 / Recombinant expression: No
MassTheoretical: 22.631727 kDa
SourceSpecies: Toxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /

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Component #11: protein, Ribosomal protein eS8

ProteinName: Ribosomal protein eS8 / Recombinant expression: No
MassTheoretical: 23.615604 kDa
SourceSpecies: Toxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /

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Component #12: protein, Ribosomal protein uS4

ProteinName: Ribosomal protein uS4 / Recombinant expression: No
MassTheoretical: 21.731396 kDa
SourceSpecies: Toxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /

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Component #13: protein, Ribosomal protein eS10

ProteinName: Ribosomal protein eS10 / Recombinant expression: No
MassTheoretical: 17.428098 kDa
SourceSpecies: Toxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /

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Component #14: protein, Ribosomal protein uS17

ProteinName: Ribosomal protein uS17 / Recombinant expression: No
MassTheoretical: 18.715984 kDa
SourceSpecies: Toxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /

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Component #15: protein, Ribosomal protein eS12

ProteinName: Ribosomal protein eS12 / Recombinant expression: No
MassTheoretical: 15.419675 kDa
SourceSpecies: Toxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /

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Component #16: protein, Ribosomal protein uS15

ProteinName: Ribosomal protein uS15 / Recombinant expression: No
MassTheoretical: 17.211363 kDa
SourceSpecies: Toxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /

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Component #17: protein, Ribosomal protein uS11

ProteinName: Ribosomal protein uS11 / Recombinant expression: No
MassTheoretical: 16.330598 kDa
SourceSpecies: Toxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /

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Component #18: protein, Ribosomal protein uS19

ProteinName: Ribosomal protein uS19 / Recombinant expression: No
MassTheoretical: 17.190223 kDa
SourceSpecies: Toxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /

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Component #19: protein, Ribosomal protein uS9

ProteinName: Ribosomal protein uS9 / Recombinant expression: No
MassTheoretical: 16.587488 kDa
SourceSpecies: Toxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /

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Component #20: protein, Ribosomal protein eS17

ProteinName: Ribosomal protein eS17 / Recombinant expression: No
MassTheoretical: 15.256675 kDa
SourceSpecies: Toxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /

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Component #21: protein, Ribosomal protein uS13

ProteinName: Ribosomal protein uS13 / Recombinant expression: No
MassTheoretical: 17.761662 kDa
SourceSpecies: Toxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /

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Component #22: protein, Ribosomal protein eS19

ProteinName: Ribosomal protein eS19 / Recombinant expression: No
MassTheoretical: 18.414312 kDa
SourceSpecies: Toxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /

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Component #23: protein, Ribosomal protein uS10

ProteinName: Ribosomal protein uS10 / Recombinant expression: No
MassTheoretical: 25.943293 kDa
SourceSpecies: Toxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /

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Component #24: protein, Ribosomal protein eS21

ProteinName: Ribosomal protein eS21 / Recombinant expression: No
MassTheoretical: 9.049265 kDa
SourceSpecies: Toxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /

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Component #25: protein, Ribosomal protein uS8

ProteinName: Ribosomal protein uS8 / Recombinant expression: No
MassTheoretical: 14.973676 kDa
SourceSpecies: Toxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /

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Component #26: protein, Ribosomal protein uS12

ProteinName: Ribosomal protein uS12 / Recombinant expression: No
MassTheoretical: 15.837605 kDa
SourceSpecies: Toxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /

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Component #27: protein, Ribosomal protein eS24

ProteinName: Ribosomal protein eS24 / Recombinant expression: No
MassTheoretical: 15.23091 kDa
SourceSpecies: Toxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /

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Component #28: protein, Ribosomal protein eS25

ProteinName: Ribosomal protein eS25 / Recombinant expression: No
MassTheoretical: 18.707014 kDa
SourceSpecies: Toxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /

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Component #29: protein, Ribosomal protein eS26

ProteinName: Ribosomal protein eS26 / Recombinant expression: No
MassTheoretical: 12.75363 kDa
SourceSpecies: Toxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /

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Component #30: protein, Ribosomal protein eS27

ProteinName: Ribosomal protein eS27 / Recombinant expression: No
MassTheoretical: 9.10585 kDa
SourceSpecies: Toxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /

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Component #31: protein, Ribosomal protein eS28

ProteinName: Ribosomal protein eS28 / Recombinant expression: No
MassTheoretical: 7.601858 kDa
SourceSpecies: Toxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /

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Component #32: protein, Ribosomal protein uS14

ProteinName: Ribosomal protein uS14 / Recombinant expression: No
MassTheoretical: 6.533824 kDa
SourceSpecies: Toxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /

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Component #33: protein, Ribosomal protein eS30

ProteinName: Ribosomal protein eS30 / Recombinant expression: No
MassTheoretical: 6.6198 kDa
SourceSpecies: Toxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /

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Component #34: protein, Ribosomal protein eS31

ProteinName: Ribosomal protein eS31 / Recombinant expression: No
MassTheoretical: 17.353152 kDa
SourceSpecies: Toxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /

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Component #35: protein, Ribosomal protein eL41

ProteinName: Ribosomal protein eL41 / Recombinant expression: No
MassTheoretical: 5.120324 kDa
SourceSpecies: Toxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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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: 2 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 108162
3D reconstructionResolution: 3.35 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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