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- PDB-5xyi: Small subunit of Trichomonas vaginalis ribosome -

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Entry
Database: PDB / ID: 5xyi
TitleSmall subunit of Trichomonas vaginalis ribosome
Components
  • (40S ribosomal protein ...) x 15
  • (Ribosomal protein ...) x 10
  • (Uncharacterized ...) x 5
  • 18S
  • Guanine nucleotide-binding protein beta subunit, putative
  • Plectin/S10 domain containing protein
  • eL41
KeywordsRIBOSOME / Trichomonas vaginalis ribosome / rRNA / rprotein
Function / homologyRibosomal protein S2, eukaryotic / WD40-repeat-containing domain superfamily / 30s ribosomal protein S13, C-terminal / Ribosomal protein S10 domain / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S28e conserved site / 50S ribosomal protein L30e-like / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / Ribosomal protein S8 superfamily ...Ribosomal protein S2, eukaryotic / WD40-repeat-containing domain superfamily / 30s ribosomal protein S13, C-terminal / Ribosomal protein S10 domain / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S28e conserved site / 50S ribosomal protein L30e-like / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / Ribosomal protein S8 superfamily / Winged helix-like DNA-binding domain superfamily / Ribosomal protein S2, flavodoxin-like domain 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 / Ribosomal protein S11 superfamily / RNA-binding S4 domain superfamily / 40S Ribosomal protein S10 / Ribosomal protein S7 domain / Ribosomal protein S19, superfamily / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S17e, conserved site / K homology domain-like, alpha/beta / WD40-repeat-containing domain / Ribosomal protein S4, conserved site / Ribosomal S11, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S15P / WD40 repeat, conserved site / Ribosomal protein S17, conserved site / G-protein beta WD-40 repeat / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S4/S9 / Ribosomal protein S19e domain superfamily / Ribosomal protein S26e superfamily / Ribosomal protein S11 signature. / Plectin/S10 domain / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein S21e / Ribosomal protein S7e / Ribosomal protein S24e / Ribosomal protein S26e / S4 domain / Ribosomal protein S27 / S25 ribosomal protein / Ribosomal protein S5, C-terminal domain / Ribosomal protein S28e / 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 S7 signature. / Ribosomal protein S8e / Ribosomal protein S6e / Ribosomal protein S21e superfamily / Ribosomal protein S5, N-terminal domain / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S12/S23 / Ribosomal protein S7p/S5e / Ribosomal protein S3, C-terminal domain / Ribosomal protein S19 / Ribosomal protein S14p/S29e / Ribosomal protein S15 / Ribosomal protein S2 / Ribosomal protein S10p/S20e / Ribosomal protein S19e / Ribosomal protein S17 / Ribosomal protein S9/S16 / WD domain, G-beta repeat / Ribosomal protein S8 / Ribosomal protein S11 / Ribosomal protein S13/S18 / Ribosomal S17 / Ribosomal family S4e / Ribosomal S3Ae family / WD40/YVTN repeat-like-containing domain superfamily / Ribosomal protein L2, domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S8 / Ribosomal protein S5/S7 / Ribosomal protein S17/S11 / Ribosomal protein S28e / Ribosomal protein S12e / Ribosomal protein S7e / Ribosomal protein S15 / Ribosomal protein S27e / Ribosomal protein S9
Function and homology information
Specimen sourceTrichomonas vaginalis (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.35 Å resolution
AuthorsLi, Z. / Guo, Q. / Zheng, L. / Ji, Y. / Xie, Y. / Lai, D. / Lun, Z. / Suo, X. / Gao, N.
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 8, 2017 / Release: Aug 30, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 30, 2017Structure modelrepositoryInitial release
1.1Oct 18, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Assembly

Deposited unit
2: 18S
A: 40S ribosomal protein SA
B: Ribosomal protein S3Ae, putative
C: Uncharacterized protein
D: Ribosomal protein S3, putative
E: 40S ribosomal protein S4
F: 40s ribosomal protein S5-B, putative
G: 40S ribosomal protein S6
H: 40S ribosomal protein S7, putative
I: 40S ribosomal protein S8
J: Uncharacterized protein
K: Plectin/S10 domain containing protein
L: Uncharacterized protein
M: Ribosomal protein L7Ae, putative
N: 40S ribosomal protein S13, putative
O: Ribosomal protein S14
P: Ribosomal protein S19, putative
Q: 40S ribosomal protein S16, putative
R: 40S ribosomal protein S17-B, putative
S: Ribosomal protein S13p/S18e, putative
T: Ribosomal protein S19e, putative
U: Ribosomal protein S10p/S20e, putative
V: 40S ribosomal protein S21
W: Ribosomal protein S15a
X: 40S ribosomal protein S23, putative
Y: Ribosomal protein S24e, putative
Z: Uncharacterized protein
a: 40S ribosomal protein S26
b: 40S ribosomal protein S27
c: Uncharacterized protein
d: 40S ribosomal protein S29, putative
e: 40S ribosomal protein S30
g: Guanine nucleotide-binding protein beta subunit, putative
n: eL41


Theoretical massNumber of molelcules
Total (without water)1,088,12134
Polyers1,088,12134
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 1 types, 1 molecules 2

#1: RNA chain 18S


Mass: 508656.188 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote)

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40S ribosomal protein ... , 15 types, 15 molecules AEFGHINQRVXabde

#2: Protein/peptide 40S ribosomal protein SA / / uS2


Mass: 28584.676 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2EFE7
#6: Protein/peptide 40S ribosomal protein S4 / / eS4


Mass: 28589.561 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2FC75
#7: Protein/peptide 40s ribosomal protein S5-B, putative / Ribosome / uS7


Mass: 21672.889 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2E4S6
#8: Protein/peptide 40S ribosomal protein S6 / / eS6


Mass: 24583.883 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2DEJ9
#9: Protein/peptide 40S ribosomal protein S7, putative / Ribosome / eS7


Mass: 18708.568 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2G5X6
#10: Protein/peptide 40S ribosomal protein S8 / / eS8


Mass: 22118.488 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2E1L5
#15: Protein/peptide 40S ribosomal protein S13, putative / Ribosome / uS15


Mass: 17071.031 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2D9L2
#18: Protein/peptide 40S ribosomal protein S16, putative / Ribosome / uS9


Mass: 15626.175 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2D919
#19: Protein/peptide 40S ribosomal protein S17-B, putative / Ribosome / eS17


Mass: 14964.434 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2DPS3
#23: Protein/peptide 40S ribosomal protein S21 / / eS21


Mass: 9853.130 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2FFS8
#25: Protein/peptide 40S ribosomal protein S23, putative / Ribosome / uS12


Mass: 15592.457 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2D895
#28: Protein/peptide 40S ribosomal protein S26 / / eS26


Mass: 13889.256 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2DST7
#29: Protein/peptide 40S ribosomal protein S27 / / eS27


Mass: 9467.907 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2FBZ2
#31: Protein/peptide 40S ribosomal protein S29, putative / Ribosome / uS14


Mass: 6843.100 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2DYA8
#32: Protein/peptide 40S ribosomal protein S30 / / eS30


Mass: 6919.079 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2FHY5

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Ribosomal protein ... , 10 types, 10 molecules BDMOPSTUWY

#3: Protein/peptide Ribosomal protein S3Ae, putative / Ribosome / eS1


Mass: 28085.471 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2G9Z8
#5: Protein/peptide Ribosomal protein S3, putative / Ribosome / uS3


Mass: 24505.658 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2DIM3
#14: Protein/peptide Ribosomal protein L7Ae, putative / Ribosome / eS12


Mass: 13714.954 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2FA40
#16: Protein/peptide Ribosomal protein S14 / / uS11


Mass: 16689.012 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: Q76KS8
#17: Protein/peptide Ribosomal protein S19, putative / Ribosome / uS19


Mass: 16286.080 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2DVD8
#20: Protein/peptide Ribosomal protein S13p/S18e, putative / Ribosome / uS13


Mass: 17564.523 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2DTR8
#21: Protein/peptide Ribosomal protein S19e, putative / Ribosome / eS19


Mass: 16584.188 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2EG54
#22: Protein/peptide Ribosomal protein S10p/S20e, putative / Ribosome / uS10


Mass: 13933.201 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2FDE0
#24: Protein/peptide Ribosomal protein S15a / Ribosome / uS8


Mass: 14583.213 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2DLW4
#26: Protein/peptide Ribosomal protein S24e, putative / Ribosome / eS24


Mass: 16069.884 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2F0H5

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Uncharacterized ... , 5 types, 5 molecules CJLZc

#4: Protein/peptide Uncharacterized protein / uS5


Mass: 30083.736 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2EHK3
#11: Protein/peptide Uncharacterized protein / uS4


Mass: 21811.295 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2DNY3
#13: Protein/peptide Uncharacterized protein / uS17


Mass: 18015.252 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2DHU8
#27: Protein/peptide Uncharacterized protein / eS25


Mass: 12645.859 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2ER97
#30: Protein/peptide Uncharacterized protein / eS28


Mass: 7650.717 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2DQN8

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Protein/peptide , 3 types, 3 molecules Kgn

#12: Protein/peptide Plectin/S10 domain containing protein / eS10


Mass: 16251.438 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2EBA2
#33: Protein/peptide Guanine nucleotide-binding protein beta subunit, putative / RACK1


Mass: 37151.832 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2ELV7
#34: Protein/peptide eL41


Mass: 3354.243 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: P0CX86*PLUS

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Small subunit of Trichomonas vaginalis ribosome / Type: RIBOSOME
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34
Source: NATURAL
Source (natural)Organism: Trichomonas vaginalis (eukaryote)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 57162 / Symmetry type: POINT

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