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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
DescriptorUncharacterized protein
Plectin/S10 domain containing protein
Guanine nucleotide-binding protein beta subunit
eL41/RNA Complex
(40S ribosomal protein ...) x 15
(Ribosomal protein ...) x 10
KeywordsRIBOSOME / Trichomonas vaginalis ribosome / rRNA / rprotein
Specimen sourceTrichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス
MethodElectron microscopy (3.35 Å resolution / Particle / Single particle)
AuthorsLi, Z. / Guo, Q. / Zheng, L. / Ji, Y. / Xie, Y. / Lai, D. / Lun, Z. / Suo, X. / Gao, N.
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 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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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 chain18S


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

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

#2: Polypeptide(L)40S ribosomal protein SA / uS2


Mass: 28584.676 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2EFE7

Cellular component

Molecular function

Biological process

  • endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000447)
  • endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000461)
  • ribosomal small subunit assembly (GO: 0000028)
  • rRNA export from nucleus (GO: 0006407)
  • translation (GO: 0006412)
#6: Polypeptide(L)40S ribosomal protein S4 / eS4


Mass: 28589.561 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2FC75

Cellular component

Molecular function

Biological process

#7: Polypeptide(L)40s ribosomal protein S5-B, putative / uS7


Mass: 21672.889 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2E4S6

Cellular component

Molecular function

Biological process

#8: Polypeptide(L)40S ribosomal protein S6 / eS6


Mass: 24583.883 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2DEJ9

Cellular component

Molecular function

Biological process

#9: Polypeptide(L)40S ribosomal protein S7, putative / eS7


Mass: 18708.568 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2G5X6

Cellular component

Molecular function

Biological process

#10: Polypeptide(L)40S ribosomal protein S8 / eS8


Mass: 22118.488 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2E1L5

Cellular component

Molecular function

Biological process

  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
  • translation (GO: 0006412)
#15: Polypeptide(L)40S ribosomal protein S13, putative / uS15


Mass: 17071.031 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2D9L2

Cellular component

Molecular function

Biological process

#18: Polypeptide(L)40S ribosomal protein S16, putative / uS9


Mass: 15626.175 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2D919

Cellular component

Molecular function

Biological process

  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
  • translation (GO: 0006412)
#19: Polypeptide(L)40S ribosomal protein S17-B, putative / eS17


Mass: 14964.434 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2DPS3

Cellular component

Molecular function

Biological process

#23: Polypeptide(L)40S ribosomal protein S21 / eS21


Mass: 9853.130 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2FFS8

Cellular component

Molecular function

Biological process

  • endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000447)
  • endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000461)
  • translation (GO: 0006412)
#25: Polypeptide(L)40S ribosomal protein S23, putative / uS12


Mass: 15592.457 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2D895

Cellular component

Molecular function

Biological process

#28: Polypeptide(L)40S ribosomal protein S26 / eS26


Mass: 13889.256 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2DST7

Cellular component

Molecular function

Biological process

#29: Polypeptide(L)40S ribosomal protein S27 / eS27


Mass: 9467.907 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2FBZ2

Cellular component

Molecular function

Biological process

#31: Polypeptide(L)40S ribosomal protein S29, putative / uS14


Mass: 6843.100 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2DYA8

Cellular component

Molecular function

Biological process

#32: Polypeptide(L)40S ribosomal protein S30 / eS30


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

Cellular component

Molecular function

Biological process

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

#3: Polypeptide(L)Ribosomal protein S3Ae, putative / eS1


Mass: 28085.471 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2G9Z8

Cellular component

Molecular function

Biological process

#5: Polypeptide(L)Ribosomal protein S3, putative / uS3


Mass: 24505.658 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2DIM3

Cellular component

Molecular function

Biological process

#14: Polypeptide(L)Ribosomal protein L7Ae, putative / eS12


Mass: 13714.954 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2FA40

Cellular component

Molecular function

Biological process

#16: Polypeptide(L)Ribosomal protein S14 / uS11


Mass: 16689.012 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: Q76KS8

Cellular component

Molecular function

Biological process

  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
  • ribosomal small subunit assembly (GO: 0000028)
  • translation (GO: 0006412)
#17: Polypeptide(L)Ribosomal protein S19, putative / uS19


Mass: 16286.080 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2DVD8

Cellular component

Molecular function

Biological process

#20: Polypeptide(L)Ribosomal protein S13p/S18e, putative / uS13


Mass: 17564.523 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2DTR8

Cellular component

Molecular function

Biological process

#21: Polypeptide(L)Ribosomal protein S19e, putative / eS19


Mass: 16584.188 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2EG54

Cellular component

Molecular function

Biological process

#22: Polypeptide(L)Ribosomal protein S10p/S20e, putative / uS10


Mass: 13933.201 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2FDE0

Cellular component

Molecular function

Biological process

#24: Polypeptide(L)Ribosomal protein S15a / uS8


Mass: 14583.213 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2DLW4

Cellular component

Molecular function

Biological process

#26: Polypeptide(L)Ribosomal protein S24e, putative / eS24


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

Cellular component

Molecular function

Biological process

  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
  • translation (GO: 0006412)

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Uncharacterized ... , 5 types, 5 molecules CJLZc

#4: Polypeptide(L)Uncharacterized protein / uS5


Mass: 30083.736 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2EHK3

Cellular component

Molecular function

Biological process

#11: Polypeptide(L)Uncharacterized protein / uS4


Mass: 21811.295 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2DNY3

Cellular component

Molecular function

Biological process

#13: Polypeptide(L)Uncharacterized protein / uS17


Mass: 18015.252 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2DHU8

Cellular component

Molecular function

Biological process

#27: Polypeptide(L)Uncharacterized protein / eS25


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


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

Cellular component

Molecular function

Biological process

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Polypeptide(L) , 3 types, 3 molecules Kgn

#12: Polypeptide(L)Plectin/S10 domain containing protein / eS10


Mass: 16251.438 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2EBA2

Cellular component

Molecular function

Biological process

#33: Polypeptide(L)Guanine nucleotide-binding protein beta subunit, putative / RACK1


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


Mass: 3354.243 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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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
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 FIELD
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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