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- EMDB-6784: Large subunit of Trichomonas vaginalis ribosome -

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Basic information

Entry
Database: EMDB / ID: 6784
TitleLarge subunit of Trichomonas vaginalis ribosome
SampleLarge subunit of Trichomonas vaginalis ribosome
SourceTrichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス
Map data
Methodsingle particle reconstruction, at 3.2 Å resolution
AuthorsLi Z / Guo Q
CitationCell Res., 2017

Cell Res., 2017 StrPapers
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: 5xy3

SummaryFull reportAbout validation report
DateDeposition: Jul 6, 2017 / Header (metadata) release: Aug 30, 2017 / Map release: Aug 30, 2017 / Last update: Sep 6, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.044
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 0.044
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5xy3
  • Surface level: 0.044
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_6784.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:0.044 (by author), 0.044 (movie #1):
Minimum - Maximum-0.23113365 - 0.39924592
Average (Standard dev.)0.0004943846 (0.01008034)
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-190-190-190
NX/NY/NZ380380380
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.2310.3990.000

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Supplemental data

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Mask #1

Fileemd_6784_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_6784_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire Large subunit of Trichomonas vaginalis ribosome

EntireName: Large subunit of Trichomonas vaginalis ribosome / Number of components: 44

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Component #1: protein, Large subunit of Trichomonas vaginalis ribosome

ProteinName: Large subunit of Trichomonas vaginalis ribosome / Recombinant expression: No
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #2: nucleic-acid, 25S ribosomal RNA

Nucleic-acidName: 25S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CGUAGUCUGC CAUACGCAGG AAGACCCGCU GAACUGAAGC AUCUCAUUAA GCGGAGGAAA AGAAACUAAC UAGGAUUCCC UUAGUAAAGG CGAUCGAAAA GGGAACAGCC CAACGUCUUA AUCCCGCAAG GGAAAUGUAG UCGGUUCACC UAUUGCACUG GUCUAAGUCA GAUGGAAUGC UGCGCGAUUC AGAGUAAAAG CCUCGUAUGA CCAACCGCAA GCUUACGAUG GACCGGGGAG AGUCGGAUAC UUUGAGAGUA GUGUCUUAAG GGGGUGGUAU GUCCCAUCCA AGGCUAAAUA ACGUGAGGAG ACCGAUAGAU UACAAGUAGU GUGAACGAAA GAUGAAAAGA ACUCUAAAAC AGAGGGUGAA AAGUUCCUGA ACUUGCUUAG GGUUAAGGCU AUUUAUAGUA CCCGUCUUGA AACACGGAUU AGGGAGUUUA UCUGUAGUGC GAGUCUUUGC ACGUUAACUG UAAAGGCGUA GAGAAAGCAA CUGGCGUUUG CAUGGCUACU GAGCAUUACU GAUAGGACCC GAAAGGUGGU GAACUUUGCC UGCACAGGUU GAAGUCAGGG GAAACUCUGA UGGAGGACCG UACGGGUUAU UGAUGUGCAA AUCAUUUUUC UGAUGUAGGU AAAGGUGCGA AAGACUCAUC GAACCACCUA AUAGCUGGUU UCCUCCGAAG UUUCCCUCAG GAUAGCUGUA AUGCAUUUAG UUAAGGGGAG UAGAGAUAUG GGUAGAGGUG CAGGGAGCCU UCGGGUUCUC AACUUAUUUC CAAACUUCGA ACCUCCUUGU UAGGCAUUUA CCUAACUGGA AAUGCUUAAA UGAAUUAGCG UUACAAGUGG GCUCUGACCG GUAAGCGGUC AUGGCGAAAU GGGAUGAACC AUACGUCUGA AUAAGGUGCC GAAAUGUACU AUCACUGAUA CCAUAAAGGG AGUCCAUGUA UUUAGACAGC AGGUCGGUGC CCCUAAAAGC AGGUAUCCGC UAAAGAGUGU GUUAAAACUC ACCUGCCGAA UACUAGGGCC CCGAAAAUGA AUGGCGCAUA UAGUACUACC GAUCUCAGAC AUCAGUUCUA UUGAACUGAG AGUAGGGGGA UGUGGACAUU UUUGUGAAGG UGCAAUGUGA GUUGGACUGG AAGAAUGUCU AUUACAGAUC CUAAUUGAAG UAGCGAUUAU CCAGGCUUGU AUCCUGGGGG CUGAUGAGGA GUAGGGUUUC UGGACAACUU AAACAGAUCC AGAGUUAGUC GAUCCUAAUC UCAAUAAUGG GAGAAAGGGA GUACAGUUGA UAUUCUGUAA CUGACAACAG UUCGCGGCAA CGCAUACUAU UUUUCUCCGC CAAUCUUAUA CCGUUGGUAG GGAUCUCUUU CCUACAUGAC AGUACUAAUA CCCAGGGAAA CUGGUCAUCA GGCGAACUGC GGCGUUCUGC UGGCAAAACA UAGCUUCGGU UAUGUCAAUG GCUAUUGGAU UGGUCCAUGA AGCGAAAAAU AGUUUACUGU GUCACUCGUA CCGAUAACCG CAUCAGGUCU UCUAGGUAAG UAGCCUAUGG CCAUUGAGGC AUGAUAGUUC AGGGAAUUCG GCCAAUUAGA GCUGUAACUU CGGGAUAAAG CUUGGCUCUG AUGAAAAUCA GAACCGAUUG UUACGCGGAG AGCCCAACUG UUUAAUAAAA ACGUAGUGUC GCGCUGUGGU AGUAUAGCCA GUGAACGCGA CAUGAAUCCU GCUCAGUGCU GUGUCUGUUA AUAUGGUUCA AGCCAACGAA GCACCGGUAA AUAGCUGGGG UAACUAUGAC UCUUAUCAAA GUAGCGAAAU ACCUCGUCAC UUAAUUAGUG ACCUGCAUGA ACGGAGCUAU GAGGUUCUCA CUGUCCCAAA CUGUCUCUCA GCGAACCAAC UGUAGUGGGA ACGGUCACUA GAUAUCCAGC GGGGAAAGAA GACCCUGUAG AGCUUCACUU UGGUCUAGUC UUGUAUAGUU CCUGCGGGGG UGUAGACUAG GUGGGAGAGC AAUCGAUUCU GAAAAACCAC UACCCUGUUU GGAAUUAUGC UUACCUAUCA CAAGGAAUAG GACUAGAUAG AAAGUUUGGC UGGGGCGGCA CACCUUCGAA AGAGCAGCGA AGGUGUCCUA AGUUGAGCUC AGUGAGGACA GAAAUCUCAC GUUGAGGAUA AGGCCAAAAG CUCAAUUUAC UGUGCCUUUU UGUACUAGGA UCAGUUACGA AAGUAAGGCC UAACGAUCCC UAAAUAGCCU CAGGUGCGUG AGGAUUGGGG UGACAGACAA GUUACCUCCG GGACAACUGG CUUGUGGCUG CUAAGAGAUC AAAUCAACGC AGCUUUUUGA UUCUUCGAUG UCGGCUCUUC CUAUCCUAGU GAUGUACAAG UUGCUAAGGG UCGGAUUGUU CACCCGUAUU AGGGAUCGUG AGCUGGGUUU AGACCGUCGU GAGCCAGGUU UGUUUUAUCC UACUGGAUAU AGCAUCAUGA UAGUAGAUUG AUUUAGUACG AGAGGAACUG UUGAUUAUGG CCUCUGGUUA GCGAUUAUCG GAAACGGUAU GUCGCGCAGC UACGCCGUCU GGGAUAAUGG CUGAAAGCCU CUUAAGCCAG AAGCCCAUCU AGAAAGUGAU GCACGUGAUG UUGGACCGAU ACGAAUAAUC AUACUCAAAA GGUCCGCUUC AUAGGUAACC CAAUGUAGAA GACAUUGUGU GAACGAAGGU ACUGUAAGCA GUGGAGUGGC AUUACGUCCA CGACCUGUUG AGGUUCAGCU UCGCUUCUAG GUUUCCAAAU AUUUU
MassTheoretical: 892.223312 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #3: nucleic-acid, 5S ribosomal RNA

Nucleic-acidName: 5S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GAAGCGGCCA CACCCGGCUG GCAACAUCCA GCUCCACUCC GAACCUGGAA AUUAAGCAGU CGCGGGCCAC AUCAGUACUG GGCUGGGCGA CUUCCCGGGA ACGUGCGGUG CUUGCUUC
MassTheoretical: 37.963594 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #4: nucleic-acid, 5.8S ribosomal RNA

Nucleic-acidName: 5.8S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AAGUCUCUAA GCAAUGGAUG UCUUGGCUCC UCACACGAUG AAGAACGUGG CAUAAUGUGU UAAGUAACCG GAGUUGCAAA CAUCAUGACA GGUUAAUCUU UGAAUGCAAA UUGCGCUAAA CUCGAUCUCG GUCGAGAAGC AUGGGUGUGA CAGUACUACA UC
MassTheoretical: 52.173945 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #5: protein, Ribosomal protein L8, putative

ProteinName: Ribosomal protein L8, putative / Recombinant expression: No
MassTheoretical: 26.949082 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #6: protein, Uncharacterized protein

ProteinName: Uncharacterized protein / Recombinant expression: No
MassTheoretical: 46.90427 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #7: protein, Ribosomal protein, putative

ProteinName: Ribosomal protein, putative / Recombinant expression: No
MassTheoretical: 40.320738 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #8: protein, Ribosomal protein L5

ProteinName: Ribosomal protein L5 / Recombinant expression: No
MassTheoretical: 34.932766 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #9: protein, 60S ribosomal protein L6, putative

ProteinName: 60S ribosomal protein L6, putative / Recombinant expression: No
MassTheoretical: 16.045772 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #10: protein, Ribosomal protein L30p/L7e, putative

ProteinName: Ribosomal protein L30p/L7e, putative / Recombinant expression: No
MassTheoretical: 26.842281 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #11: protein, Ribosomal protein L7Ae, putative

ProteinName: Ribosomal protein L7Ae, putative / Recombinant expression: No
MassTheoretical: 27.602273 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #12: protein, Ribosomal protein L6, putative

ProteinName: Ribosomal protein L6, putative / Recombinant expression: No
MassTheoretical: 22.930506 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #13: protein, Ribosomal protein, putative

ProteinName: Ribosomal protein, putative / Recombinant expression: No
MassTheoretical: 23.800781 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #14: protein, 60S ribosomal protein L11, putative

ProteinName: 60S ribosomal protein L11, putative / Recombinant expression: No
MassTheoretical: 19.373488 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #15: protein, Ribosomal protein L13e, putative

ProteinName: Ribosomal protein L13e, putative / Recombinant expression: No
MassTheoretical: 21.865705 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #16: protein, Ribosomal protein L14, putative

ProteinName: Ribosomal protein L14, putative / Recombinant expression: No
MassTheoretical: 14.726112 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #17: protein, Ribosomal protein L15

ProteinName: Ribosomal protein L15 / Recombinant expression: No
MassTheoretical: 24.323465 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #18: protein, Ribosomal protein L13, putative

ProteinName: Ribosomal protein L13, putative / Recombinant expression: No
MassTheoretical: 22.569111 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #19: protein, Ribosomal protein L22, putative

ProteinName: Ribosomal protein L22, putative / Recombinant expression: No
MassTheoretical: 18.53049 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #20: protein, 60S ribosomal protein L18, putative

ProteinName: 60S ribosomal protein L18, putative / Recombinant expression: No
MassTheoretical: 21.122545 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #21: protein, 60S ribosomal protein L19-3, putative

ProteinName: 60S ribosomal protein L19-3, putative / Recombinant expression: No
MassTheoretical: 21.056785 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #22: protein, 60S ribosomal protein L18a

ProteinName: 60S ribosomal protein L18a / Recombinant expression: No
MassTheoretical: 19.853973 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #23: protein, Ribosomal protein L21e, putative

ProteinName: Ribosomal protein L21e, putative / Recombinant expression: No
MassTheoretical: 17.910867 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #24: protein, 60S ribosomal protein L22-1, putative

ProteinName: 60S ribosomal protein L22-1, putative / Recombinant expression: No
MassTheoretical: 12.237054 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #25: protein, 60S ribosomal protein L23, putative

ProteinName: 60S ribosomal protein L23, putative / Recombinant expression: No
MassTheoretical: 14.840554 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #26: protein, Ribosomal protein L24e, putative

ProteinName: Ribosomal protein L24e, putative / Recombinant expression: No
MassTheoretical: 13.282475 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #27: protein, Ribosomal protein L23, putative

ProteinName: Ribosomal protein L23, putative / Recombinant expression: No
MassTheoretical: 15.582249 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #28: protein, Ribosomal protein L24, putative

ProteinName: Ribosomal protein L24, putative / Recombinant expression: No
MassTheoretical: 15.782617 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #29: protein, Ribosomal protein L27e, putative

ProteinName: Ribosomal protein L27e, putative / Recombinant expression: No
MassTheoretical: 15.946061 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #30: protein, Uncharacterized protein

ProteinName: Uncharacterized protein / Recombinant expression: No
MassTheoretical: 17.006787 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #31: protein, 60S ribosomal protein L29

ProteinName: 60S ribosomal protein L29 / Recombinant expression: No
MassTheoretical: 6.823724 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #32: protein, 60S ribosomal protein L30, putative

ProteinName: 60S ribosomal protein L30, putative / Recombinant expression: No
MassTheoretical: 12.316229 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #33: protein, Ribosomal protein L31e, putative

ProteinName: Ribosomal protein L31e, putative / Recombinant expression: No
MassTheoretical: 12.446528 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #34: protein, Ribosomal protein L32, putative

ProteinName: Ribosomal protein L32, putative / Recombinant expression: No
MassTheoretical: 15.249669 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #35: protein, Ribosomal protein L35Ae, putative

ProteinName: Ribosomal protein L35Ae, putative / Recombinant expression: No
MassTheoretical: 11.668678 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #36: protein, Ribosomal protein L34e, putative

ProteinName: Ribosomal protein L34e, putative / Recombinant expression: No
MassTheoretical: 13.346646 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #37: protein, Ribosomal protein L29, putative

ProteinName: Ribosomal protein L29, putative / Recombinant expression: No
MassTheoretical: 14.300049 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #38: protein, Ribosomal protein L36e, putative

ProteinName: Ribosomal protein L36e, putative / Recombinant expression: No
MassTheoretical: 10.941717 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #39: protein, Ribosomal protein L37

ProteinName: Ribosomal protein L37 / Recombinant expression: No
MassTheoretical: 9.355945 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #40: protein, Ribosomal protein L38e, putative

ProteinName: Ribosomal protein L38e, putative / Recombinant expression: No
MassTheoretical: 8.46896 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #41: protein, 60S ribosomal protein L39, putative

ProteinName: 60S ribosomal protein L39, putative / Recombinant expression: No
MassTheoretical: 6.297775 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #42: protein, Ubiquitin, putative

ProteinName: Ubiquitin, putative / Recombinant expression: No
MassTheoretical: 15.101515 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #43: protein, 60S ribosomal protein L44, putative

ProteinName: 60S ribosomal protein L44, putative / Recombinant expression: No
MassTheoretical: 12.471015 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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Component #44: protein, Uncharacterized protein

ProteinName: Uncharacterized protein / Recombinant expression: No
MassTheoretical: 10.051994 kDa
SourceSpecies: Trichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス

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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: 57162
3D reconstructionResolution: 3.2 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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