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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
Map data
SampleSmall subunit of Toxoplasma gondii ribosome:
nucleic-acidNucleic acid / (Ribosomal protein ...) x 33
Function / homologyRibosomal protein S11 superfamily / Ribosomal protein S5, N-terminal domain / Ribosomal protein S12/S23 / Ribosomal protein S7p/S5e / Ribosomal protein S3, C-terminal domain / Ribosomal protein S19 / Ubiquitin family / Ribosomal protein S14p/S29e / Ribosomal protein S15 / Ribosomal protein S2 ...Ribosomal protein S11 superfamily / Ribosomal protein S5, N-terminal domain / Ribosomal protein S12/S23 / Ribosomal protein S7p/S5e / Ribosomal protein S3, C-terminal domain / Ribosomal protein S19 / Ubiquitin family / Ribosomal protein S14p/S29e / Ribosomal protein S15 / Ribosomal protein S2 / Ribosomal protein S10p/S20e / S27a-like superfamily / Ribosomal protein S17 / Ribosomal protein S9/S16 / Ribosomal protein S8 / Ribosomal protein S11 / Ribosomal protein S13/S18 / KOW motif / Ribosomal S17 / Ribosomal family S4e / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S21e superfamily / Ribosomal protein S19e / Ribosomal protein S8 superfamily / Ribosomal protein S2, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S28e conserved site / 50S ribosomal protein L30e-like / Ubiquitin-like domain superfamily / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / Winged helix-like DNA-binding domain superfamily / Ribosomal protein S26e superfamily / Winged helix DNA-binding domain superfamily / Ribosomal protein S17e-like superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S10 domain superfamily / RNA-binding S4 domain superfamily / 40S Ribosomal protein S10 / Ribosomal protein S19e domain superfamily / Ribosomal protein S4e, central domain superfamily / Ribosomal S3Ae family / Ribosomal protein S6e / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13 signature. / Ribosomal protein S19 signature. / Ribosomal protein S9 signature. / Ribosomal protein S15 signature. / Ribosomal protein S14 signature. / Ribosomal protein S4e signature. / Ribosomal protein S24e signature. / Ribosomal protein S6e signature. / Ribosomal protein S4 signature. / Ribosomal protein S17e signature. / Ribosomal protein S12 signature. / Ribosomal protein S26e signature. / Ribosomal protein S28e signature. / Ribosomal protein S2 signature 1. / Ribosomal protein S2 signature 2. / Ribosomal protein S21e signature. / Ribosomal protein S12e signature. / Ubiquitin domain profile. / Ribosomal protein S13 family profile. / Ribosomal protein S17 signature. / Ribosomal protein S11 signature. / Ribosomal protein S28e / Ribosomal protein S27 / Ribosomal protein S8e / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein S21e / Ribosomal protein S7e / Ribosomal protein S24e / Ribosomal protein S26e / S4 domain / Ribosomal protein S27a / S25 ribosomal protein / Ribosomal protein S7 signature. / Plectin/S10 domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S30 / Ribosomal protein L41 / KH domain / Ribosomal S13/S15 N-terminal domain / RS4NT (NUC023) domain / 40S ribosomal protein S4 C-terminus / Ribosomal_S17 N-terminal / Ribosomal protein S10 domain / Ribosomal protein S7 domain / S5 double stranded RNA-binding domain profile. / Ribosomal protein S27a / Ribosomal protein S2 / Ribosomal protein S13 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S21e / Ribosomal protein S11 / Ribosomal protein S24e / Ribosomal protein S19/S15 / RNA-binding S4 domain
Function and homology information
SourceToxoplasma gondii (eukaryote)
Methodsingle particle reconstruction / cryo EM / 3.35 Å resolution
AuthorsLI Z / Guo Q
CitationJournal: Cell Res. / Year: 2017
Title: Cryo-EM structures of the 80S ribosomes from human parasites Trichomonas vaginalis and Toxoplasma gondii.
Authors: Zhifei Li / Qiang Guo / Lvqin Zheng / Yongsheng Ji / Yi-Ting Xie / De-Hua Lai / Zhao-Rong Lun / Xun Suo / Ning Gao
Abstract: As an indispensable molecular machine universal in all living organisms, the ribosome has been selected by evolution to be the natural target of many antibiotics and small-molecule inhibitors. ...As an indispensable molecular machine universal in all living organisms, the ribosome has been selected by evolution to be the natural target of many antibiotics and small-molecule inhibitors. High-resolution structures of pathogen ribosomes are crucial for understanding the general and unique aspects of translation control in disease-causing microbes. With cryo-electron microscopy technique, we have determined structures of the cytosolic ribosomes from two human parasites, Trichomonas vaginalis and Toxoplasma gondii, at resolution of 3.2-3.4 Å. Although the ribosomal proteins from both pathogens are typical members of eukaryotic families, with a co-evolution pattern between certain species-specific insertions/extensions and neighboring ribosomal RNA (rRNA) expansion segments, the sizes of their rRNAs are sharply different. Very interestingly, rRNAs of T. vaginalis are in size comparable to prokaryotic counterparts, with nearly all the eukaryote-specific rRNA expansion segments missing. These structures facilitate the dissection of evolution path for ribosomal proteins and RNAs, and may aid in design of novel translation inhibitors.
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
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  • 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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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
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.

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)

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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)

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Component #3: protein, Ribosomal protein uS2

ProteinName: Ribosomal protein uS2Ribosome / Recombinant expression: No
MassTheoretical: 31.546902 kDa
SourceSpecies: Toxoplasma gondii (eukaryote)

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Component #4: protein, Ribosomal protein eS1

ProteinName: Ribosomal protein eS1Ribosome / Recombinant expression: No
MassTheoretical: 29.425625 kDa
SourceSpecies: Toxoplasma gondii (eukaryote)

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Component #5: protein, Ribosomal protein uS5

ProteinName: Ribosomal protein uS5Ribosome / Recombinant expression: No
MassTheoretical: 29.385004 kDa
SourceSpecies: Toxoplasma gondii (eukaryote)

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Component #6: protein, Ribosomal protein uS3

ProteinName: Ribosomal protein uS3Ribosome / Recombinant expression: No
MassTheoretical: 26.117539 kDa
SourceSpecies: Toxoplasma gondii (eukaryote)

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Component #7: protein, Ribosomal protein eS4

ProteinName: Ribosomal protein eS4Ribosome / Recombinant expression: No
MassTheoretical: 30.204713 kDa
SourceSpecies: Toxoplasma gondii (eukaryote)

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Component #8: protein, Ribosomal protein uS7

ProteinName: Ribosomal protein uS7Ribosome / Recombinant expression: No
MassTheoretical: 21.650238 kDa
SourceSpecies: Toxoplasma gondii (eukaryote)

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Component #9: protein, Ribosomal protein eS6

ProteinName: Ribosomal protein eS6Ribosome / Recombinant expression: No
MassTheoretical: 29.027504 kDa
SourceSpecies: Toxoplasma gondii (eukaryote)

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Component #10: protein, Ribosomal protein eS7

ProteinName: Ribosomal protein eS7Ribosome / Recombinant expression: No
MassTheoretical: 22.631727 kDa
SourceSpecies: Toxoplasma gondii (eukaryote)

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Component #11: protein, Ribosomal protein eS8

ProteinName: Ribosomal protein eS8Ribosome / Recombinant expression: No
MassTheoretical: 23.615604 kDa
SourceSpecies: Toxoplasma gondii (eukaryote)

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Component #12: protein, Ribosomal protein uS4

ProteinName: Ribosomal protein uS4Ribosome / Recombinant expression: No
MassTheoretical: 21.731396 kDa
SourceSpecies: Toxoplasma gondii (eukaryote)

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Component #13: protein, Ribosomal protein eS10

ProteinName: Ribosomal protein eS10Ribosome / Recombinant expression: No
MassTheoretical: 17.428098 kDa
SourceSpecies: Toxoplasma gondii (eukaryote)

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Component #14: protein, Ribosomal protein uS17

ProteinName: Ribosomal protein uS17Ribosome / Recombinant expression: No
MassTheoretical: 18.715984 kDa
SourceSpecies: Toxoplasma gondii (eukaryote)

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Component #15: protein, Ribosomal protein eS12

ProteinName: Ribosomal protein eS12Ribosome / Recombinant expression: No
MassTheoretical: 15.419675 kDa
SourceSpecies: Toxoplasma gondii (eukaryote)

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Component #16: protein, Ribosomal protein uS15

ProteinName: Ribosomal protein uS15Ribosome / Recombinant expression: No
MassTheoretical: 17.211363 kDa
SourceSpecies: Toxoplasma gondii (eukaryote)

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Component #17: protein, Ribosomal protein uS11

ProteinName: Ribosomal protein uS11Ribosome / Recombinant expression: No
MassTheoretical: 16.330598 kDa
SourceSpecies: Toxoplasma gondii (eukaryote)

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Component #18: protein, Ribosomal protein uS19

ProteinName: Ribosomal protein uS19Ribosome / Recombinant expression: No
MassTheoretical: 17.190223 kDa
SourceSpecies: Toxoplasma gondii (eukaryote)

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Component #19: protein, Ribosomal protein uS9

ProteinName: Ribosomal protein uS9Ribosome / Recombinant expression: No
MassTheoretical: 16.587488 kDa
SourceSpecies: Toxoplasma gondii (eukaryote)

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Component #20: protein, Ribosomal protein eS17

ProteinName: Ribosomal protein eS17Ribosome / Recombinant expression: No
MassTheoretical: 15.256675 kDa
SourceSpecies: Toxoplasma gondii (eukaryote)

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Component #21: protein, Ribosomal protein uS13

ProteinName: Ribosomal protein uS13Ribosome / Recombinant expression: No
MassTheoretical: 17.761662 kDa
SourceSpecies: Toxoplasma gondii (eukaryote)

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Component #22: protein, Ribosomal protein eS19

ProteinName: Ribosomal protein eS19Ribosome / Recombinant expression: No
MassTheoretical: 18.414312 kDa
SourceSpecies: Toxoplasma gondii (eukaryote)

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Component #23: protein, Ribosomal protein uS10

ProteinName: Ribosomal protein uS10Ribosome / Recombinant expression: No
MassTheoretical: 25.943293 kDa
SourceSpecies: Toxoplasma gondii (eukaryote)

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Component #24: protein, Ribosomal protein eS21

ProteinName: Ribosomal protein eS21Ribosome / Recombinant expression: No
MassTheoretical: 9.049265 kDa
SourceSpecies: Toxoplasma gondii (eukaryote)

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Component #25: protein, Ribosomal protein uS8

ProteinName: Ribosomal protein uS8Ribosome / Recombinant expression: No
MassTheoretical: 14.973676 kDa
SourceSpecies: Toxoplasma gondii (eukaryote)

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Component #26: protein, Ribosomal protein uS12

ProteinName: Ribosomal protein uS12Ribosome / Recombinant expression: No
MassTheoretical: 15.837605 kDa
SourceSpecies: Toxoplasma gondii (eukaryote)

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Component #27: protein, Ribosomal protein eS24

ProteinName: Ribosomal protein eS24Ribosome / Recombinant expression: No
MassTheoretical: 15.23091 kDa
SourceSpecies: Toxoplasma gondii (eukaryote)

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Component #28: protein, Ribosomal protein eS25

ProteinName: Ribosomal protein eS25Ribosome / Recombinant expression: No
MassTheoretical: 18.707014 kDa
SourceSpecies: Toxoplasma gondii (eukaryote)

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Component #29: protein, Ribosomal protein eS26

ProteinName: Ribosomal protein eS26Ribosome / Recombinant expression: No
MassTheoretical: 12.75363 kDa
SourceSpecies: Toxoplasma gondii (eukaryote)

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Component #30: protein, Ribosomal protein eS27

ProteinName: Ribosomal protein eS27Ribosome / Recombinant expression: No
MassTheoretical: 9.10585 kDa
SourceSpecies: Toxoplasma gondii (eukaryote)

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Component #31: protein, Ribosomal protein eS28

ProteinName: Ribosomal protein eS28Ribosome / Recombinant expression: No
MassTheoretical: 7.601858 kDa
SourceSpecies: Toxoplasma gondii (eukaryote)

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Component #32: protein, Ribosomal protein uS14

ProteinName: Ribosomal protein uS14Ribosome / Recombinant expression: No
MassTheoretical: 6.533824 kDa
SourceSpecies: Toxoplasma gondii (eukaryote)

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Component #33: protein, Ribosomal protein eS30

ProteinName: Ribosomal protein eS30Ribosome / Recombinant expression: No
MassTheoretical: 6.6198 kDa
SourceSpecies: Toxoplasma gondii (eukaryote)

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Component #34: protein, Ribosomal protein eS31

ProteinName: Ribosomal protein eS31Ribosome / Recombinant expression: No
MassTheoretical: 17.353152 kDa
SourceSpecies: Toxoplasma gondii (eukaryote)

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Component #35: protein, Ribosomal protein eL41

ProteinName: Ribosomal protein eL41Ribosome / Recombinant expression: No
MassTheoretical: 5.120324 kDa
SourceSpecies: Toxoplasma gondii (eukaryote)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
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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