5XXU

Small subunit of Toxoplasma gondii 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 1.2 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
Ribosomal protein uS2B [auth A]287Toxoplasma gondiiMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS1C [auth B]259Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for B9PGG2 (Toxoplasma gondii (strain ATCC 50861 / VEG))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS5D [auth C]269Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for B9PZF2 (Toxoplasma gondii (strain ATCC 50861 / VEG))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS3E [auth D]235Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A0F7UXI8 (Toxoplasma gondii (strain ATCC 50861 / VEG))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS4F [auth E]263Toxoplasma gondiiMutation(s): 0 
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Find proteins for Q1JSZ0 (Toxoplasma gondii)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS7G [auth F]192Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS6H [auth G]256Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS7I [auth H]196Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS8J [auth I]205Toxoplasma gondiiMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS4K [auth J]188Toxoplasma gondiiMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS10L [auth K]152Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS17M [auth L]161Toxoplasma gondiiMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS12N [auth M]142Toxoplasma gondiiMutation(s): 0 
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Find proteins for B9Q056 (Toxoplasma gondii (strain ATCC 50861 / VEG))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS15O [auth N]151Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A125YSG6 (Toxoplasma gondii (strain ATCC 50861 / VEG))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS11P [auth O]156Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A125YXW4 (Toxoplasma gondii (strain ATCC 50861 / VEG))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS19Q [auth P]150Toxoplasma gondiiMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS9R [auth Q]148Toxoplasma gondiiMutation(s): 0 
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Find proteins for B6KC70 (Toxoplasma gondii (strain ATCC 50861 / VEG))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS17S [auth R]132Toxoplasma gondiiMutation(s): 0 
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Find proteins for B9PXH2 (Toxoplasma gondii)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS13T [auth S]156Toxoplasma gondiiMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS19U [auth T]160Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A125YMR9 (Toxoplasma gondii (strain ATCC 50861 / VEG))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS10V [auth U]233Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for B6KQG9 (Toxoplasma gondii (strain ATCC 50861 / VEG))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS21W [auth V]82Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A125YS47 (Toxoplasma gondii (strain ATCC 50861 / VEG))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS8X [auth W]130Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A125YJX3 (Toxoplasma gondii (strain ATCC 50861 / VEG))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS12Y [auth X]143Toxoplasma gondiiMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS24Z [auth Y]135Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for A0A125YKH1 (Toxoplasma gondii (strain ATCC 50861 / VEG))
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS25AA [auth Z]161Toxoplasma gondiiMutation(s): 0 
UniProt
Find proteins for S7V273 (Toxoplasma gondii (strain ATCC 50853 / GT1))
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS26BA [auth a]112Toxoplasma gondiiMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS27CA [auth b]82Toxoplasma gondiiMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS28DA [auth c]68Toxoplasma gondiiMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS14EA [auth d]54Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS30FA [auth e]59Toxoplasma gondiiMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS31GA [auth f]154Toxoplasma gondiiMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL41HA [auth m]39Toxoplasma gondiiMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
18S RNAA [auth 2]1,791Toxoplasma gondii
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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
  • Version 1.2: 2018-10-24
    Changes: Data collection, Refinement description