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
  • 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 L8, putativeA251Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_005910TVAG_104490TVAG_371270TVAG_484180TVAG_487750
Find proteins for A2E6Z8 (Trichomonas vaginalis)
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Go to UniProtKB:  A2E6Z8
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized proteinB415Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_013060TVAG_059650TVAG_124190
Find proteins for A2DD62 (Trichomonas vaginalis)
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Go to UniProtKB:  A2DD62
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L5D308Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_113720
Find proteins for A2DNM5 (Trichomonas vaginalis)
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Go to UniProtKB:  A2DNM5
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6, putativeE151Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_099510
Find proteins for A2FXW1 (Trichomonas vaginalis)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L30p/L7e, putativeF239Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_159370
Find proteins for A2F592 (Trichomonas vaginalis)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L7Ae, putativeG244Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_009840
Find proteins for A2ET60 (Trichomonas vaginalis)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L6, putativeH197Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_054500TVAG_198960TVAG_255140TVAG_297470
Find proteins for A2DDT1 (Trichomonas vaginalis)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein, putativeI209Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_232820
Find proteins for A2FVZ6 (Trichomonas vaginalis)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L13e, putativeL189Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_112230
Find proteins for A2G4E1 (Trichomonas vaginalis)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L14, putativeM128Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_026460
Find proteins for A2DZ49 (Trichomonas vaginalis)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L15N204Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_148950TVAG_200220TVAG_276360
Find proteins for A2ECR7 (Trichomonas vaginalis)
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L13, putativeO200Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_026230
Find proteins for A2DZ26 (Trichomonas vaginalis)
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L22, putativeP164Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_083260TVAG_109440TVAG_296170TVAG_473910
Find proteins for A2DM53 (Trichomonas vaginalis)
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19-3, putativeR178Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_006170TVAG_185160TVAG_185170TVAG_185180
Find proteins for A2D8G1 (Trichomonas vaginalis)
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L21e, putativeT159Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_231250
Find proteins for A2F2S5 (Trichomonas vaginalis)
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Go to UniProtKB:  A2F2S5
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L22-1, putativeU106Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_057020TVAG_225760
Find proteins for A2DNV5 (Trichomonas vaginalis)
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Go to UniProtKB:  A2DNV5
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23, putativeV140Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_015800TVAG_024110TVAG_074940TVAG_345430TVAG_345440TVAG_345450
Find proteins for A2DP51 (Trichomonas vaginalis)
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L24e, putativeW113Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_101690TVAG_190290TVAG_324900TVAG_431350
Find proteins for A2DJQ1 (Trichomonas vaginalis)
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L27e, putativeZ139Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_140290TVAG_215980TVAG_302830TVAG_306310TVAG_337950
Find proteins for A2DNC1 (Trichomonas vaginalis)
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized proteina151Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_121550TVAG_300490TVAG_346410TVAG_401890
Find proteins for A2DHU7 (Trichomonas vaginalis)
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29b58Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_083040TVAG_158840TVAG_451230
Find proteins for A2DM33 (Trichomonas vaginalis)
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30, putativec112Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_005920TVAG_213810
Find proteins for A2E6Z9 (Trichomonas vaginalis)
Explore A2E6Z9 
Go to UniProtKB:  A2E6Z9
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L31e, putatived110Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_076410TVAG_262240
Find proteins for A2D9N8 (Trichomonas vaginalis)
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L32, putativee132Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_265930TVAG_265950
Find proteins for A2F2J0 (Trichomonas vaginalis)
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L35Ae, putativef102Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_067370
Find proteins for A2DSF3 (Trichomonas vaginalis)
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L34e, putativeg116Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_094720TVAG_094730
Find proteins for A2FWA1 (Trichomonas vaginalis)
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Go to UniProtKB:  A2FWA1
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L36e, putativei91Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_020530TVAG_027320TVAG_207430
Find proteins for A2EXW7 (Trichomonas vaginalis)
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L37j81Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_005760TVAG_339320
Find proteins for A2F8Y8 (Trichomonas vaginalis)
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Go to UniProtKB:  A2F8Y8
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L44, putativeo104Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_034660TVAG_035120TVAG_083470TVAG_126180TVAG_136040TVAG_276010TVAG_470540TVAG_485680
Find proteins for A2DAI6 (Trichomonas vaginalis)
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Go to UniProtKB:  A2DAI6
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized proteinp92Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_083700TVAG_083720TVAG_099020TVAG_124410TVAG_212620TVAG_283240
Find proteins for A2DEM7 (Trichomonas vaginalis)
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Go to UniProtKB:  A2DEM7
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11, putativeJ169Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_044560TVAG_046840TVAG_092870TVAG_194850TVAG_343970
Find proteins for A2E7L8 (Trichomonas vaginalis)
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Go to UniProtKB:  A2E7L8
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18, putativeQ186Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_121100TVAG_395470
Find proteins for A2D7Q5 (Trichomonas vaginalis)
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Go to UniProtKB:  A2D7Q5
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18aS176Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_263760
Find proteins for A2EP03 (Trichomonas vaginalis)
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L23, putativeX140Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_160160
Find proteins for A2DUV8 (Trichomonas vaginalis)
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L24, putativeY138Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_190230
Find proteins for A2DKF2 (Trichomonas vaginalis)
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L29, putativeh124Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_158830
Find proteins for A2E6R2 (Trichomonas vaginalis)
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L38e, putativek74Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_066460
Find proteins for A2FFH9 (Trichomonas vaginalis)
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L39, putativel51Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_050420TVAG_076370TVAG_174110TVAG_224370TVAG_246600
Find proteins for A2D9N4 (Trichomonas vaginalis)
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin, putativem132Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_110140
Find proteins for A2DGL5 (Trichomonas vaginalis)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein, putativeC370Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_128790TVAG_189110
Find proteins for A2E4D0 (Trichomonas vaginalis)
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Go to UniProtKB:  A2E4D0
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Entity ID: 1
MoleculeChainsLengthOrganism
25S ribosomal RNA12765Trichomonas vaginalis

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Entity ID: 2
MoleculeChainsLengthOrganism
5S ribosomal RNA3118Trichomonas vaginalis

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Entity ID: 3
MoleculeChainsLengthOrganism
5.8S ribosomal RNA4162Trichomonas vaginalis
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 

  • 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