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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 / homology
Function and homology information


positive regulation of translational fidelity / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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) / rescue of stalled ribosome / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / protein kinase C binding / mRNA 5'-UTR binding / ribosomal small subunit biogenesis ...positive regulation of translational fidelity / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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) / rescue of stalled ribosome / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / protein kinase C binding / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA processing / cytosolic small ribosomal subunit / ribosome binding / cytoplasmic translation / small ribosomal subunit / cytosolic large ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / positive regulation of protein phosphorylation / translation / mRNA binding / nucleolus / enzyme binding / RNA binding / zinc ion binding / metal ion binding / nucleus / cytosol
Similarity search - Function
Ribosomal protein S17 / : / Ribosomal protein S26 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #1000 / Ribosomal protein S4, central domain / Ribosomal protein S21 / Alpha-Beta Plaits - #3370 / Hypothetical Cytosolic Protein; Chain: A; / Ribosomal protein S27 / first zn-finger domain of poly(adp-ribose) polymerase-1 ...Ribosomal protein S17 / : / Ribosomal protein S26 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #1000 / Ribosomal protein S4, central domain / Ribosomal protein S21 / Alpha-Beta Plaits - #3370 / Hypothetical Cytosolic Protein; Chain: A; / Ribosomal protein S27 / first zn-finger domain of poly(adp-ribose) polymerase-1 / Diphtheria Toxin Repressor; domain 2 / : / Ribosomal protein S3, C-terminal domain / Ribosomal Protein S14/S29 / 30s Ribosomal Protein S14; Chain N / Ribosomal Protein S8; Chain: A, domain 1 - #30 / RNA-binding S4 domain / Ribosomal Protein S7 / Ribosomal protein S7/S5 / Ribosomal protein S3 C-terminal domain / Dna Ligase; domain 1 - #10 / Ribosomal protein S11/S14 / Ribosomal protein S10 / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / S15/NS1, RNA-binding / SH3 type barrels. - #30 / K homology (KH) domain / Double Stranded RNA Binding Domain - #20 / Helicase, Ruva Protein; domain 3 - #50 / Glucose-6-phosphate isomerase like protein; domain 1 / Ribosomal Protein S8; Chain: A, domain 1 / Ribosomal Protein S5; domain 2 - #10 / N-terminal domain of TfIIb / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S12e / GMP Synthetase; Chain A, domain 3 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S19e, conserved site / Ribosomal protein S26e / Ribosomal Protein S5; domain 2 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / Ribosomal protein S17e, conserved site / Ribosomal protein S2, eukaryotic / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / S25 ribosomal protein / Ribosomal protein S19A/S15e / Ribosomal protein S30 / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S5, eukaryotic/archaeal / Double Stranded RNA Binding Domain / 40S ribosomal protein S11, N-terminal / Ribosomal protein S6, eukaryotic / Ribosomal protein S7e / 40S ribosomal protein S4, C-terminal domain / Ribosomal S17 / Ribosomal protein S19e signature. / Ribosomal protein S19e / 40S Ribosomal protein S10 / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S27 / Ribosomal protein S28e conserved site / Ribosomal protein S28e / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal_S17 N-terminal / Plectin/S10, N-terminal / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal protein S7e / YVTN repeat-like/Quinoprotein amine dehydrogenase / Plectin/S10 domain / Ribosomal protein S8e / Ribosomal protein S4, KOW domain / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S6e / Ribosomal protein S4/S9, eukaryotic/archaeal / RS4NT (NUC023) domain / Ribosomal protein S27 / Ribosomal S3Ae family
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S23, putative / 40S ribosomal protein S16, putative / 40S ribosomal protein S13, putative / 40S ribosomal protein S6 / Ribosomal_S17_N domain-containing protein / Ribosomal protein S3, putative ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S23, putative / 40S ribosomal protein S16, putative / 40S ribosomal protein S13, putative / 40S ribosomal protein S6 / Ribosomal_S17_N domain-containing protein / Ribosomal protein S3, putative / Ribosomal protein S15a / Ribosomal_S4 domain-containing protein / 40S ribosomal protein S17-B, putative / Uncharacterized protein / 40S ribosomal protein S26 / Ribosomal protein S13p/S18e, putative / Ribosomal protein S19, putative / 40S ribosomal protein S29, putative / 40S ribosomal protein S8 / 40s ribosomal protein S5-B, putative / Plectin/S10 domain containing protein / 40S ribosomal protein SA / Ribosomal protein S19e, putative / S5 DRBM domain-containing protein / Guanine nucleotide-binding protein beta subunit, putative / 40S ribosomal protein S25 / Ribosomal protein S24e, putative / Ribosomal protein L7Ae, putative / 40S ribosomal protein S27 / 40S ribosomal protein S4 / Ribosomal protein S10p/S20e, putative / 40S ribosomal protein S21 / 40S ribosomal protein S30 / 40S ribosomal protein S7 / Ribosomal protein S3Ae, putative / Small ribosomal subunit protein eS32A / Ribosomal protein S14
Similarity search - Component
Biological speciesTrichomonas vaginalis (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.35 Å
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 /
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. High- ...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.
History
DepositionJul 8, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
Polymers1,088,12134
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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

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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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

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

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


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


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


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


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


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


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


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


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


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


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

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Uncharacterized ... , 5 types, 5 molecules CJLZc

#4: Protein Uncharacterized protein / uS5


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


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


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


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


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

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Protein , 2 types, 2 molecules Kg

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


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


Mass: 37151.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2ELV7

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RNA chain / Protein/peptide , 2 types, 2 molecules 2n

#1: RNA chain 18S


Mass: 508656.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote)
#34: Protein/peptide eL41


Mass: 3354.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source / 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 / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Small subunit of Trichomonas vaginalis ribosome / Type: RIBOSOME / Entity ID: all / 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
MicroscopyModel: 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 / Num. of particles: 57162 / Symmetry type: POINT

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