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
  • 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 ...

    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 LengthOrganismDetailsImage
Ribosomal protein uL2D [auth A]260Toxoplasma gondiiMutation(s): 0 
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Entity ID: 5
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Ribosomal protein uL3E [auth B]389Toxoplasma gondiiMutation(s): 0 
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Entity ID: 6
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Ribosomal protein uL4F [auth C]416Toxoplasma gondiiMutation(s): 0 
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Entity ID: 7
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Ribosomal protein uL18G [auth D]310Toxoplasma gondiiMutation(s): 0 
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Entity ID: 8
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Ribosomal protein eL6H [auth E]193Toxoplasma gondiiMutation(s): 0 
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Entity ID: 9
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Ribosomal protein uL30I [auth F]258Toxoplasma gondiiMutation(s): 0 
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Entity ID: 10
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Ribosomal protein eL8J [auth G]276Toxoplasma gondiiMutation(s): 0 
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Entity ID: 11
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Ribosomal protein uL6K [auth H]190Toxoplasma gondiiMutation(s): 0 
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Entity ID: 12
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Ribosomal protein uL16L [auth I]221Toxoplasma gondiiMutation(s): 0 
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Entity ID: 13
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Ribosomal protein uL5M [auth J]175Toxoplasma gondiiMutation(s): 0 
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Entity ID: 14
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Ribosomal protein eL13N [auth K]355Toxoplasma gondiiMutation(s): 0 
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Entity ID: 15
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Ribosomal protein eL14O [auth L]134Toxoplasma gondiiMutation(s): 0 
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Entity ID: 16
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Ribosomal protein eL15P [auth M]205Toxoplasma gondiiMutation(s): 0 
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Entity ID: 17
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Ribosomal protein uL13Q [auth N]269Toxoplasma gondiiMutation(s): 0 
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Entity ID: 18
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Ribosomal protein uL22R [auth O]195Toxoplasma gondiiMutation(s): 0 
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Entity ID: 19
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Ribosomal protein eL18S [auth P]187Toxoplasma gondiiMutation(s): 0 
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Entity ID: 20
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Ribosomal protein eL19T [auth Q]187Toxoplasma gondiiMutation(s): 0 
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Entity ID: 21
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Ribosomal protein eL20U [auth R]183Toxoplasma gondiiMutation(s): 0 
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Entity ID: 22
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Ribosomal protein eL21V [auth S]157Toxoplasma gondiiMutation(s): 0 
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Entity ID: 23
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Ribosomal protein eL22W [auth T]133Toxoplasma gondiiMutation(s): 0 
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Entity ID: 24
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Ribosomal protein uL14X [auth U]139Toxoplasma gondiiMutation(s): 0 
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Entity ID: 25
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Ribosomal protein eL24Y [auth V]155Toxoplasma gondiiMutation(s): 0 
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Entity ID: 26
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Ribosomal protein uL23Z [auth W]167Toxoplasma gondiiMutation(s): 0 
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Entity ID: 27
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Ribosomal protein uL24AA [auth X]141Toxoplasma gondiiMutation(s): 0 
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Entity ID: 28
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Ribosomal protein eL27BA [auth Y]146Toxoplasma gondiiMutation(s): 0 
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Entity ID: 29
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Ribosomal protein uL15CA [auth Z]147Toxoplasma gondiiMutation(s): 0 
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Entity ID: 30
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Ribosomal protein eL29DA [auth a]54Toxoplasma gondiiMutation(s): 0 
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Entity ID: 31
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Ribosomal protein eL30EA [auth b]108Toxoplasma gondiiMutation(s): 0 
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Entity ID: 32
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Ribosomal protein eL31FA [auth c]120Toxoplasma gondiiMutation(s): 0 
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Entity ID: 33
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Ribosomal protein eL32GA [auth d]134Toxoplasma gondiiMutation(s): 0 
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Entity ID: 34
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Ribosomal protein eL33HA [auth e]112Toxoplasma gondiiMutation(s): 0 
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Entity ID: 35
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Ribosomal protein eL34IA [auth f]134Toxoplasma gondiiMutation(s): 0 
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Entity ID: 36
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Ribosomal protein uL29JA [auth g]123Toxoplasma gondiiMutation(s): 0 
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Entity ID: 37
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Ribosomal protein eL36KA [auth h]101Toxoplasma gondiiMutation(s): 0 
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Entity ID: 38
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Ribosomal protein eL37LA [auth i]98Toxoplasma gondiiMutation(s): 0 
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Entity ID: 39
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Ribosomal protein eL38MA [auth j]84Toxoplasma gondiiMutation(s): 0 
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Entity ID: 40
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Ribosomal protein eL39NA [auth k]51Toxoplasma gondiiMutation(s): 0 
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Entity ID: 41
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Ribosomal protein eL40OA [auth l]129Toxoplasma gondiiMutation(s): 0 
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Entity ID: 42
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Ribosomal protein eL42PA [auth n]105Toxoplasma gondiiMutation(s): 0 
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Entity ID: 43
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Ribosomal protein eL43QA [auth o]96Toxoplasma gondiiMutation(s): 0 
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Entity ID: 44
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Ribosomal protein eL28RA [auth p]129Toxoplasma gondiiMutation(s): 0 
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Entity ID: 1
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25S RNAA [auth 1]3477Toxoplasma gondii
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Entity ID: 2
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5S RNAB [auth 3]124Toxoplasma gondii
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Entity ID: 3
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5.8S RNAC [auth 4]158Toxoplasma gondii
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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  (Full details and data files)

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