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: 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 L8, putativeD [auth A]251Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_005910TVAG_104490TVAG_371270TVAG_484180TVAG_487750
UniProt
Find proteins for A2E6Z8 (Trichomonas vaginalis)
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UniProt GroupA2E6Z8
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinE [auth B]415Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_013060TVAG_059650TVAG_124190
UniProt
Find proteins for A2DD62 (Trichomonas vaginalis)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein, putativeF [auth C]370Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_128790TVAG_189110
UniProt
Find proteins for A2E4D0 (Trichomonas vaginalis)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L5G [auth D]308Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_113720
UniProt
Find proteins for A2DNM5 (Trichomonas vaginalis)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L6, putativeH [auth E]151Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_099510
UniProt
Find proteins for A2FXW1 (Trichomonas vaginalis)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L30p/L7e, putativeI [auth F]239Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_159370
UniProt
Find proteins for A2F592 (Trichomonas vaginalis)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L7Ae, putativeJ [auth G]244Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_009840
UniProt
Find proteins for A2ET60 (Trichomonas vaginalis)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L6, putativeK [auth H]197Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_054500TVAG_198960TVAG_255140TVAG_297470
UniProt
Find proteins for A2DDT1 (Trichomonas vaginalis)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein, putativeL [auth I]209Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_232820
UniProt
Find proteins for A2FVZ6 (Trichomonas vaginalis)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L11, putativeM [auth J]169Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_044560TVAG_046840TVAG_092870TVAG_194850TVAG_343970
UniProt
Find proteins for A2E7L8 (Trichomonas vaginalis)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L13e, putativeN [auth L]189Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_112230
UniProt
Find proteins for A2G4E1 (Trichomonas vaginalis)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L14, putativeO [auth M]128Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_026460
UniProt
Find proteins for A2DZ49 (Trichomonas vaginalis)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L15P [auth N]204Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_148950TVAG_200220TVAG_276360
UniProt
Find proteins for A2ECR7 (Trichomonas vaginalis)
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L13, putativeQ [auth O]200Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_026230
UniProt
Find proteins for A2DZ26 (Trichomonas vaginalis)
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L22, putativeR [auth P]164Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_083260TVAG_109440TVAG_296170TVAG_473910
UniProt
Find proteins for A2DM53 (Trichomonas vaginalis)
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L18, putativeS [auth Q]186Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_121100TVAG_395470
UniProt
Find proteins for A2D7Q5 (Trichomonas vaginalis)
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L19-3, putativeT [auth R]178Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_006170TVAG_185160TVAG_185170TVAG_185180
UniProt
Find proteins for A2D8G1 (Trichomonas vaginalis)
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L18aU [auth S]176Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_263760
UniProt
Find proteins for A2EP03 (Trichomonas vaginalis)
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L21e, putativeV [auth T]159Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_231250
UniProt
Find proteins for A2F2S5 (Trichomonas vaginalis)
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L22-1, putativeW [auth U]106Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_057020TVAG_225760
UniProt
Find proteins for A2DNV5 (Trichomonas vaginalis)
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L23, putativeX [auth V]140Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_015800TVAG_024110TVAG_074940TVAG_345430TVAG_345440TVAG_345450
UniProt
Find proteins for A2DP51 (Trichomonas vaginalis)
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L24e, putativeY [auth W]113Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_101690TVAG_190290TVAG_324900TVAG_431350
UniProt
Find proteins for A2DJQ1 (Trichomonas vaginalis)
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L23, putativeZ [auth X]140Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_160160
UniProt
Find proteins for A2DUV8 (Trichomonas vaginalis)
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L24, putativeAA [auth Y]138Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_190230
UniProt
Find proteins for A2DKF2 (Trichomonas vaginalis)
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L27e, putativeBA [auth Z]139Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_140290TVAG_215980TVAG_302830TVAG_306310TVAG_337950
UniProt
Find proteins for A2DNC1 (Trichomonas vaginalis)
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinCA [auth a]151Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_121550TVAG_300490TVAG_346410TVAG_401890
UniProt
Find proteins for A2DHU7 (Trichomonas vaginalis)
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L29DA [auth b]58Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_083040TVAG_158840TVAG_451230
UniProt
Find proteins for A2DM33 (Trichomonas vaginalis)
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L30, putativeEA [auth c]112Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_005920TVAG_213810
UniProt
Find proteins for A2E6Z9 (Trichomonas vaginalis)
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L31e, putativeFA [auth d]110Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_076410TVAG_262240
UniProt
Find proteins for A2D9N8 (Trichomonas vaginalis)
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L32, putativeGA [auth e]132Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_265930TVAG_265950
UniProt
Find proteins for A2F2J0 (Trichomonas vaginalis)
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L35Ae, putativeHA [auth f]102Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_067370
UniProt
Find proteins for A2DSF3 (Trichomonas vaginalis)
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L34e, putativeIA [auth g]116Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_094720TVAG_094730
UniProt
Find proteins for A2FWA1 (Trichomonas vaginalis)
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L29, putativeJA [auth h]124Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_158830
UniProt
Find proteins for A2E6R2 (Trichomonas vaginalis)
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L36e, putativeKA [auth i]91Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_020530TVAG_027320TVAG_207430
UniProt
Find proteins for A2EXW7 (Trichomonas vaginalis)
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L37LA [auth j]81Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_005760TVAG_339320
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Find proteins for A2F8Y8 (Trichomonas vaginalis)
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L38e, putativeMA [auth k]74Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_066460
UniProt
Find proteins for A2FFH9 (Trichomonas vaginalis)
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L39, putativeNA [auth l]51Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_050420TVAG_076370TVAG_174110TVAG_224370TVAG_246600
UniProt
Find proteins for A2D9N4 (Trichomonas vaginalis)
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin, putativeOA [auth m]132Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_110140
UniProt
Find proteins for A2DGL5 (Trichomonas vaginalis)
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L44, putativePA [auth o]104Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_034660TVAG_035120TVAG_083470TVAG_126180TVAG_136040TVAG_276010TVAG_470540TVAG_485680
UniProt
Find proteins for A2DAI6 (Trichomonas vaginalis)
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinQA [auth p]92Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_083700TVAG_083720TVAG_099020TVAG_124410TVAG_212620TVAG_283240
UniProt
Find proteins for A2DEM7 (Trichomonas vaginalis)
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Entity ID: 1
MoleculeChainsLengthOrganismImage
25S ribosomal RNAA [auth 1]2,765Trichomonas vaginalis
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Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
5S ribosomal RNAB [auth 3]118Trichomonas vaginalis
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
5.8S ribosomal RNAC [auth 4]162Trichomonas vaginalis
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



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