5XYI

Small subunit of Trichomonas vaginalis ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structures of the 80S ribosomes from human parasites Trichomonas vaginalis and Toxoplasma gondii

Li, Z.Guo, Q.Zheng, L.Ji, Y.Xie, Y.T.Lai, D.H.Lun, Z.R.Suo, X.Gao, N.

(2017) Cell Res 27: 1275-1288

  • DOI: https://doi.org/10.1038/cr.2017.104
  • Primary Citation of Related Structures:  
    5XXB, 5XXU, 5XY3, 5XYI

  • PubMed 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-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.


  • Organizational Affiliation

    State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAB [auth A]256Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2EFE7 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S3Ae, putativeC [auth B]247Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2G9Z8 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinD [auth C]272Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2EHK3 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S3, putativeE [auth D]216Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2DIM3 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4F [auth E]255Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2FC75 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40s ribosomal protein S5-B, putativeG [auth F]193Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2E4S6 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6H [auth G]216Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2DEJ9 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7, putativeI [auth H]168Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2G5X6 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8J [auth I]197Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2E1L5 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinK [auth J]185Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2DNY3 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Plectin/S10 domain containing proteinL [auth K]141Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2EBA2 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinM [auth L]155Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2DHU8 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L7Ae, putativeN [auth M]124Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2FA40 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13, putativeO [auth N]151Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2D9L2 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S14P [auth O]159Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for Q76KS8 (Trichomonas vaginalis)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S19, putativeQ [auth P]144Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2DVD8 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16, putativeR [auth Q]140Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2D919 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17-B, putativeS [auth R]129Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2DPS3 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S13p/S18e, putativeT [auth S]155Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2DTR8 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S19e, putativeU [auth T]148Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2EG54 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S10p/S20e, putativeV [auth U]123Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2FDE0 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21W [auth V]89Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2FFS8 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S15aX [auth W]130Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2DLW4 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23, putativeY [auth X]144Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2D895 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S24e, putativeZ [auth Y]140Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2F0H5 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinAA [auth Z]115Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2ER97 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26BA [auth a]118Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2DST7 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27CA [auth b]86Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2FBZ2 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinDA [auth c]68Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2DQN8 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29, putativeEA [auth d]57Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2DYA8 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30FA [auth e]62Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2FHY5 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein beta subunit, putativeGA [auth g]335Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2ELV7 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
eL41HA [auth n]25Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for P0CX86 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 1
MoleculeChains LengthOrganismImage
18SA [auth 2]1,577Trichomonas vaginalis
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2017-10-18
    Changes: Database references