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- EMDB-6788: Small subunit of Trichomonas vaginalis ribosome -

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Entry
Database: EMDB / ID: 6788
TitleSmall subunit of Trichomonas vaginalis ribosome
SampleSmall 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 3.35 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: 5xyi

SummaryFull reportAbout validation report
DateDeposition: Jul 8, 2017 / Header (metadata) release: Aug 30, 2017 / Map release: Aug 30, 2017 / Last update: Aug 30, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.036
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 0.036
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5xyi
  • Surface level: 0.036
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_6788.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:0.036 (by author), 0.036 (movie #1):
Minimum - Maximum-0.13911201 - 0.26773617
Average (Standard dev.)0.00029812296 (0.005232952)
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-0.1390.2680.000

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Supplemental data

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Mask #1

Fileemd_6788_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_6788_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 Trichomonas vaginalis ribosome

EntireName: Small subunit of Trichomonas vaginalis ribosome / Number of components: 35

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

ProteinName: Small 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, 18S

Nucleic-acidName: 18S / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
ACUUGGUUGA UCCUGCCAAG GAAGCACACU UAGGUCAUAG AUUAAGCCAU GCAAGUGUUA GUUCAGGUAA CGAAACUGCG AAUAGCUCAU UAAUACGCUC AGAAUCUAUU UGGCGGCGAC CAACAGGUCU UAAAUGGAUA GCAGCAGCAA CUCUGGUGCU AAUACAUGCG AUUGUUUCUC CAGAUGUGAA UUAUGGAGGA AAAGUUGACC UCAUCAGAGG CACGCCAUUC GACUGAGUGA CCUAUCAGCU UGUACUUAGG GUCUUUACCU AGGUAGGCUA UCACGGGUAA CGGGCGGUUA CCGUCGGACU GCCGGAGAAG GCGCCUGAGA GAUAGCGACU AUAUCCACGG GUAGCAGCAG GCGCGAAACU UUCCCACUCG AGACUUUCGG AGGAGGUAAU GACCAGUUCC AUUGGUGCCU UUUGGUACUG UGGAUAGGGG UACGGUUUUC CACCGUACCG AAACCUAGCA GAGGGCCAGU CUGGUGCCAG CAGCUGCGGU AAUUCCAGCU CUGCGAGUUU GCUCCCAUAU UGUUGCAGUU AAAACGCCCG UAGUCUGAAU UGGCCAGCAA UGGUCGUACG UAUUUUUACG UUCACUGUGA ACAAAUCAGG ACGCUUAGAG UAUGGCCACA UGAAUGACUC AGCGCAGUAU GAAGUCUUUG UUUUCUUCCG AAAACAAGCU CAAUGAGAGC CAUCGGGGGU AGAUCUAUCU CAUGACGAGU GGUGGAAUAC UUUGACUCAU GAGAGAGAAG CUGAGGCGAA GGCGUCUACC UAGAGGGUUU CUGUCGAUCA AGGGCGAGAG UAGGAGUAUC CAACAGGAUU AGAGACCCUG GUAGUUCCUA CCUUAAACGA UGCCGACAGG AGUUUGUCAU UUGUUAAUGG CAGAAUCUUU GGAGAAAUCA UAGUUCUUGG GCUCUGGGGG AAAUACGACC GCAAGGCUGA AACUUGAAGG AAUUGACGGA AGGGCACACC AGGGGUGGAG CCUGUGGCUU AAUUUGAAUC AACACGGGGA AACUACCCAG GACCAGAUGU UUUUUAUGAC UGACAGGCUU CGGGUCUUUC AGGAUAUUGU UUUUGGUGGU GCAUGGCCGU UGGUGGUGCG UGGGUUGACC UGUCUAGCGU UGAUUCAGCU AACGAGCGAG AUUAUCGCCA AUUAUUUACU UUGCCGAAGU CCUUCGGUUA AAGUUCUAAU UGGGACUCCC UGCGAUUUUA GCAGGUGGAA GAGGGUAGCA AUAACAGGUC CGUGAUGCCC UUUAGAUGCU CUGGGCUGCA CGCGUGCUAC AAUGUUAGGA UCAAUAGGAC UGCGAGCCUG AGAGGGUGCG CUACUCUUAU AAUCCCUAAC GUAGUUGGGA UUGACGUUUG UAAUCAGCGU CAUGAACCAG GAAUCCCUUG UAAAUGUGUG UCAACAACGC ACGUUGAAUA CGUCCCUGCC CUUUGUACAC ACCGCCCGUC GCUCCUACCG AUUGGAUGAC UCGGUGAAAU CACCGGAUGC UUACGAGCAG AAAGUGAUUA AAUCACGUUA UCUAGAGGAA GGAGAAGUCG UAACAAGGUA ACGGUAGGUG AACCUGCCGU UGGAUCA
MassTheoretical: 508.656188 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: protein, 40S ribosomal protein SA

ProteinName: 40S ribosomal protein SA / Recombinant expression: No
MassTheoretical: 28.584676 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: protein, Ribosomal protein S3Ae, putative

ProteinName: Ribosomal protein S3Ae, putative / Recombinant expression: No
MassTheoretical: 28.085471 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, Uncharacterized protein

ProteinName: Uncharacterized protein / Recombinant expression: No
MassTheoretical: 30.083736 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, Ribosomal protein S3, putative

ProteinName: Ribosomal protein S3, putative / Recombinant expression: No
MassTheoretical: 24.505658 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, 40S ribosomal protein S4

ProteinName: 40S ribosomal protein S4 / Recombinant expression: No
MassTheoretical: 28.589561 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, 40s ribosomal protein S5-B, putative

ProteinName: 40s ribosomal protein S5-B, putative / Recombinant expression: No
MassTheoretical: 21.672889 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, 40S ribosomal protein S6

ProteinName: 40S ribosomal protein S6 / Recombinant expression: No
MassTheoretical: 24.583883 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, 40S ribosomal protein S7, putative

ProteinName: 40S ribosomal protein S7, putative / Recombinant expression: No
MassTheoretical: 18.708568 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, 40S ribosomal protein S8

ProteinName: 40S ribosomal protein S8 / Recombinant expression: No
MassTheoretical: 22.118488 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, Uncharacterized protein

ProteinName: Uncharacterized protein / Recombinant expression: No
MassTheoretical: 21.811295 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, Plectin/S10 domain containing protein

ProteinName: Plectin/S10 domain containing protein / Recombinant expression: No
MassTheoretical: 16.251438 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, Uncharacterized protein

ProteinName: Uncharacterized protein / Recombinant expression: No
MassTheoretical: 18.015252 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 L7Ae, putative

ProteinName: Ribosomal protein L7Ae, putative / Recombinant expression: No
MassTheoretical: 13.714954 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, 40S ribosomal protein S13, putative

ProteinName: 40S ribosomal protein S13, putative / Recombinant expression: No
MassTheoretical: 17.071031 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 S14

ProteinName: Ribosomal protein S14 / Recombinant expression: No
MassTheoretical: 16.689012 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 S19, putative

ProteinName: Ribosomal protein S19, putative / Recombinant expression: No
MassTheoretical: 16.28608 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, 40S ribosomal protein S16, putative

ProteinName: 40S ribosomal protein S16, putative / Recombinant expression: No
MassTheoretical: 15.626175 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, 40S ribosomal protein S17-B, putative

ProteinName: 40S ribosomal protein S17-B, putative / Recombinant expression: No
MassTheoretical: 14.964434 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, Ribosomal protein S13p/S18e, putative

ProteinName: Ribosomal protein S13p/S18e, putative / Recombinant expression: No
MassTheoretical: 17.564523 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, Ribosomal protein S19e, putative

ProteinName: Ribosomal protein S19e, putative / Recombinant expression: No
MassTheoretical: 16.584188 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 S10p/S20e, putative

ProteinName: Ribosomal protein S10p/S20e, putative / Recombinant expression: No
MassTheoretical: 13.933201 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, 40S ribosomal protein S21

ProteinName: 40S ribosomal protein S21 / Recombinant expression: No
MassTheoretical: 9.85313 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, Ribosomal protein S15a

ProteinName: Ribosomal protein S15a / Recombinant expression: No
MassTheoretical: 14.583213 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, 40S ribosomal protein S23, putative

ProteinName: 40S ribosomal protein S23, putative / Recombinant expression: No
MassTheoretical: 15.592457 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 S24e, putative

ProteinName: Ribosomal protein S24e, putative / Recombinant expression: No
MassTheoretical: 16.069884 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, Uncharacterized protein

ProteinName: Uncharacterized protein / Recombinant expression: No
MassTheoretical: 12.645859 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, 40S ribosomal protein S26

ProteinName: 40S ribosomal protein S26 / Recombinant expression: No
MassTheoretical: 13.889256 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, 40S ribosomal protein S27

ProteinName: 40S ribosomal protein S27 / Recombinant expression: No
MassTheoretical: 9.467907 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, Uncharacterized protein

ProteinName: Uncharacterized protein / Recombinant expression: No
MassTheoretical: 7.650717 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, 40S ribosomal protein S29, putative

ProteinName: 40S ribosomal protein S29, putative / Recombinant expression: No
MassTheoretical: 6.8431 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, 40S ribosomal protein S30

ProteinName: 40S ribosomal protein S30 / Recombinant expression: No
MassTheoretical: 6.919079 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, Guanine nucleotide-binding protein beta subunit, putative

ProteinName: Guanine nucleotide-binding protein beta subunit, putative
Recombinant expression: No
MassTheoretical: 37.151832 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, eL41

ProteinName: eL41 / Recombinant expression: No
MassTheoretical: 3.354243 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: 3.35 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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