5XYI

Small subunit of Trichomonas vaginalis 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 1.1 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: 3
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S3Ae, putativeB247Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_047460
Find proteins for A2G9Z8 (Trichomonas vaginalis)
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Go to UniProtKB:  A2G9Z8
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized proteinC272Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_142440
Find proteins for A2EHK3 (Trichomonas vaginalis)
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Go to UniProtKB:  A2EHK3
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4E255Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_335480
Find proteins for A2FC75 (Trichomonas vaginalis)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
40s ribosomal protein S5-B, putativeF193Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_246200
Find proteins for A2E4S6 (Trichomonas vaginalis)
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Go to UniProtKB:  A2E4S6
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S7, putativeH168Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_143030TVAG_375490
Find proteins for A2G5X6 (Trichomonas vaginalis)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized proteinL155Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_113950TVAG_131850TVAG_313300TVAG_401900TVAG_419520
Find proteins for A2DHU8 (Trichomonas vaginalis)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L7Ae, putativeM124Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_010250
Find proteins for A2FA40 (Trichomonas vaginalis)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13, putativeN151Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_066760TVAG_076150TVAG_151780TVAG_459150
Find proteins for A2D9L2 (Trichomonas vaginalis)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S14O159Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_117480
Find proteins for Q76KS8 (Trichomonas vaginalis)
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S19, putativeP144Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_055940TVAG_074310TVAG_126060TVAG_208960
Find proteins for A2DVD8 (Trichomonas vaginalis)
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16, putativeQ140Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_020040TVAG_036220TVAG_036300TVAG_094760TVAG_156650TVAG_182810
Find proteins for A2D919 (Trichomonas vaginalis)
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S13p/S18e, putativeS155Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_020480TVAG_065040TVAG_184530TVAG_341090TVAG_419040TVAG_487360TVAG_487930
Find proteins for A2DTR8 (Trichomonas vaginalis)
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S19e, putativeT148Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_352520TVAG_352560TVAG_352580TVAG_352600
Find proteins for A2EG54 (Trichomonas vaginalis)
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S21V89Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_022100
Find proteins for A2FFS8 (Trichomonas vaginalis)
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S15aW130Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_006250TVAG_462530
Find proteins for A2DLW4 (Trichomonas vaginalis)
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23, putativeX144Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_071920TVAG_109530TVAG_109730TVAG_159830TVAG_198620TVAG_249090TVAG_305300TVAG_430260
Find proteins for A2D895 (Trichomonas vaginalis)
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized proteinZ115Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_226630
Find proteins for A2ER97 (Trichomonas vaginalis)
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S26a118Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_040120TVAG_061920TVAG_164600TVAG_242190TVAG_277940TVAG_302160TVAG_333200TVAG_335820TVAG_347960
Find proteins for A2DST7 (Trichomonas vaginalis)
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27b86Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_064320
Find proteins for A2FBZ2 (Trichomonas vaginalis)
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Go to UniProtKB:  A2FBZ2
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized proteinc68Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_050990TVAG_057380TVAG_266850TVAG_272940TVAG_272950TVAG_327180
Find proteins for A2DQN8 (Trichomonas vaginalis)
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S29, putatived57Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_107660TVAG_131520TVAG_357220TVAG_366620TVAG_393120TVAG_490210
Find proteins for A2DYA8 (Trichomonas vaginalis)
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein beta subunit, putativeg335Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_151920
Find proteins for A2ELV7 (Trichomonas vaginalis)
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
eL41n25Trichomonas vaginalisMutation(s): 0 
Find proteins for P0CX86 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S8I197Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_066030TVAG_164160TVAG_206300TVAG_435430
Find proteins for A2E1L5 (Trichomonas vaginalis)
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Go to UniProtKB:  A2E1L5
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized proteinJ185Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_010560TVAG_495360
Find proteins for A2DNY3 (Trichomonas vaginalis)
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Go to UniProtKB:  A2DNY3
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Plectin/S10 domain containing proteinK141Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_329340
Find proteins for A2EBA2 (Trichomonas vaginalis)
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Go to UniProtKB:  A2EBA2
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S17-B, putativeR129Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_040820TVAG_258150TVAG_453470TVAG_474010
Find proteins for A2DPS3 (Trichomonas vaginalis)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein SAA256Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_240050TVAG_474410
Find proteins for A2EFE7 (Trichomonas vaginalis)
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Go to UniProtKB:  A2EFE7
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S10p/S20e, putativeU123Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_086300
Find proteins for A2FDE0 (Trichomonas vaginalis)
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S24e, putativeY140Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_272960TVAG_272970TVAG_272980TVAG_386300
Find proteins for A2F0H5 (Trichomonas vaginalis)
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Go to UniProtKB:  A2F0H5
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S30e62Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_222910
Find proteins for A2FHY5 (Trichomonas vaginalis)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S3, putativeD216Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_106800TVAG_178710TVAG_263040TVAG_314710TVAG_420140TVAG_462690
Find proteins for A2DIM3 (Trichomonas vaginalis)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S6G216Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_033590TVAG_282960TVAG_462810TVAG_486930
Find proteins for A2DEJ9 (Trichomonas vaginalis)
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Entity ID: 1
MoleculeChainsLengthOrganism
18S21577Trichomonas vaginalis
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 

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