5XXB

Large subunit of Toxoplasma gondii ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.17 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: 10.1038/cr.2017.104
  • Structures With Same Primary Citation

  • 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 cruc ...

    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, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL2A260Toxoplasma gondiiMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL3B389Toxoplasma gondiiMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL4C416Toxoplasma gondiiMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL18D310Toxoplasma gondiiMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL6E193Toxoplasma gondiiMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL30F258Toxoplasma gondiiMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL8G276Toxoplasma gondiiMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL6H190Toxoplasma gondiiMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL16I221Toxoplasma gondiiMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL5J175Toxoplasma gondiiMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL13K355Toxoplasma gondiiMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL14L134Toxoplasma gondiiMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL15M205Toxoplasma gondiiMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL13N269Toxoplasma gondiiMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL22O195Toxoplasma gondiiMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL18P187Toxoplasma gondiiMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL19Q187Toxoplasma gondiiMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL20R183Toxoplasma gondiiMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL21S157Toxoplasma gondiiMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL22T133Toxoplasma gondiiMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL14U139Toxoplasma gondiiMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL24V155Toxoplasma gondiiMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL24X141Toxoplasma gondiiMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL27Y146Toxoplasma gondiiMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL29a54Toxoplasma gondiiMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL30b108Toxoplasma gondiiMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL31c120Toxoplasma gondiiMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL32d134Toxoplasma gondiiMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL33e112Toxoplasma gondiiMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL34f134Toxoplasma gondiiMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL29g123Toxoplasma gondiiMutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL36h101Toxoplasma gondiiMutation(s): 0 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL37i98Toxoplasma gondiiMutation(s): 0 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL40l129Toxoplasma gondiiMutation(s): 0 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL43o96Toxoplasma gondiiMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL28p129Toxoplasma gondiiMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL23W167Toxoplasma gondiiMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL15Z147Toxoplasma gondiiMutation(s): 0 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL38j84Toxoplasma gondiiMutation(s): 0 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL39k51Toxoplasma gondiiMutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL42n105Toxoplasma gondiiMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganism
25S RNA13477Toxoplasma gondii

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Entity ID: 2
MoleculeChainsLengthOrganism
5S RNA3124Toxoplasma gondii

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Entity ID: 3
MoleculeChainsLengthOrganism
5.8S RNA4158Toxoplasma gondii
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.17 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

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