5XY3

Large subunit of Trichomonas vaginalis ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L8, putativeD [auth A]251Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2E6Z8 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinE [auth B]415Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2DD62 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein, putativeF [auth C]370Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2E4D0 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L5G [auth D]308Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2DNM5 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6, putativeH [auth E]151Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2FXW1 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L30p/L7e, putativeI [auth F]239Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2F592 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L7Ae, putativeJ [auth G]244Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2ET60 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L6, putativeK [auth H]197Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2DDT1 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein, putativeL [auth I]209Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2FVZ6 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11, putativeM [auth J]169Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2E7L8 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L13e, putativeN [auth L]189Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2G4E1 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L14, putativeO [auth M]128Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2DZ49 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15P [auth N]204Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2ECR7 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L13, putativeQ [auth O]200Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2DZ26 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L22, putativeR [auth P]164Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2DM53 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18, putativeS [auth Q]186Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2D7Q5 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19-3, putativeT [auth R]178Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2D8G1 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aU [auth S]176Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2EP03 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L21e, putativeV [auth T]159Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2F2S5 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22-1, putativeW [auth U]106Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2DNV5 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23, putativeX [auth V]140Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2DP51 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L24e, putativeY [auth W]113Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2DJQ1 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L23, putativeZ [auth X]140Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2DUV8 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L24, putativeAA [auth Y]138Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2DKF2 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L27e, putativeBA [auth Z]139Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2DNC1 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinCA [auth a]151Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2DHU7 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29DA [auth b]58Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2DM33 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30, putativeEA [auth c]112Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2E6Z9 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L31e, putativeFA [auth d]110Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2D9N8 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L32, putativeGA [auth e]132Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2F2J0 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L35Ae, putativeHA [auth f]102Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2DSF3 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L34e, putativeIA [auth g]116Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2FWA1 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L29, putativeJA [auth h]124Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2E6R2 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L36e, putativeKA [auth i]91Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2EXW7 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37LA [auth j]81Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2F8Y8 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L38e, putativeMA [auth k]74Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2FFH9 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39, putativeNA [auth l]51Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2D9N4 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin, putativeOA [auth m]132Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2DGL5 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L44, putativePA [auth o]104Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2DAI6 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinQA [auth p]92Trichomonas vaginalisMutation(s): 0 
UniProt
Find proteins for A2DEM7 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
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Entity ID: 1
MoleculeChains LengthOrganismImage
25S ribosomal RNAA [auth 1]2,765Trichomonas vaginalis
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S ribosomal RNAB [auth 3]118Trichomonas vaginalis
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Entity ID: 3
MoleculeChains LengthOrganismImage
5.8S ribosomal RNAC [auth 4]162Trichomonas vaginalis
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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: 2017-09-06
    Changes: Structure summary
  • Version 1.2: 2017-10-18
    Changes: Database references
  • Version 1.3: 2019-12-18
    Changes: Advisory, Derived calculations