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
  • Primary Citation of Related Structures:  
    5XY3, 5XXB, 5XYI, 5XXU

  • 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

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein SAB [auth A]256Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_240050TVAG_474410
Find proteins for A2EFE7 (Trichomonas vaginalis)
Explore A2EFE7 
Go to UniProtKB:  A2EFE7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S3Ae, putativeC [auth B]247Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_047460
Find proteins for A2G9Z8 (Trichomonas vaginalis)
Explore A2G9Z8 
Go to UniProtKB:  A2G9Z8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinD [auth C]272Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_142440
Find proteins for A2EHK3 (Trichomonas vaginalis)
Explore A2EHK3 
Go to UniProtKB:  A2EHK3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S3, putativeE [auth D]216Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_106800TVAG_178710TVAG_263040TVAG_314710TVAG_420140TVAG_462690
Find proteins for A2DIM3 (Trichomonas vaginalis)
Explore A2DIM3 
Go to UniProtKB:  A2DIM3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S4F [auth E]255Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_335480
Find proteins for A2FC75 (Trichomonas vaginalis)
Explore A2FC75 
Go to UniProtKB:  A2FC75
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40s ribosomal protein S5-B, putativeG [auth F]193Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_246200
Find proteins for A2E4S6 (Trichomonas vaginalis)
Explore A2E4S6 
Go to UniProtKB:  A2E4S6
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S6H [auth G]216Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_033590TVAG_282960TVAG_462810TVAG_486930
Find proteins for A2DEJ9 (Trichomonas vaginalis)
Explore A2DEJ9 
Go to UniProtKB:  A2DEJ9
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S7, putativeI [auth H]168Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_143030TVAG_375490
Find proteins for A2G5X6 (Trichomonas vaginalis)
Explore A2G5X6 
Go to UniProtKB:  A2G5X6
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S8J [auth I]197Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_066030TVAG_164160TVAG_206300TVAG_435430
Find proteins for A2E1L5 (Trichomonas vaginalis)
Explore A2E1L5 
Go to UniProtKB:  A2E1L5
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinK [auth J]185Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_010560TVAG_495360
Find proteins for A2DNY3 (Trichomonas vaginalis)
Explore A2DNY3 
Go to UniProtKB:  A2DNY3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Plectin/S10 domain containing proteinL [auth K]141Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_329340
Find proteins for A2EBA2 (Trichomonas vaginalis)
Explore A2EBA2 
Go to UniProtKB:  A2EBA2
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinM [auth L]155Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_113950TVAG_131850TVAG_313300TVAG_401900TVAG_419520
Find proteins for A2DHU8 (Trichomonas vaginalis)
Explore A2DHU8 
Go to UniProtKB:  A2DHU8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L7Ae, putativeN [auth M]124Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_010250
Find proteins for A2FA40 (Trichomonas vaginalis)
Explore A2FA40 
Go to UniProtKB:  A2FA40
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S13, putativeO [auth N]151Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_066760TVAG_076150TVAG_151780TVAG_459150
Find proteins for A2D9L2 (Trichomonas vaginalis)
Explore A2D9L2 
Go to UniProtKB:  A2D9L2
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S14P [auth O]159Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_117480
Find proteins for Q76KS8 (Trichomonas vaginalis)
Explore Q76KS8 
Go to UniProtKB:  Q76KS8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S19, putativeQ [auth P]144Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_055940TVAG_074310TVAG_126060TVAG_208960
Find proteins for A2DVD8 (Trichomonas vaginalis)
Explore A2DVD8 
Go to UniProtKB:  A2DVD8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S16, putativeR [auth Q]140Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_020040TVAG_036220TVAG_036300TVAG_094760TVAG_156650TVAG_182810
Find proteins for A2D919 (Trichomonas vaginalis)
Explore A2D919 
Go to UniProtKB:  A2D919
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S17-B, putativeS [auth R]129Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_040820TVAG_258150TVAG_453470TVAG_474010
Find proteins for A2DPS3 (Trichomonas vaginalis)
Explore A2DPS3 
Go to UniProtKB:  A2DPS3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S13p/S18e, putativeT [auth S]155Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_020480TVAG_065040TVAG_184530TVAG_341090TVAG_419040TVAG_487360TVAG_487930
Find proteins for A2DTR8 (Trichomonas vaginalis)
Explore A2DTR8 
Go to UniProtKB:  A2DTR8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S19e, putativeU [auth T]148Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_352520TVAG_352560TVAG_352580TVAG_352600
Find proteins for A2EG54 (Trichomonas vaginalis)
Explore A2EG54 
Go to UniProtKB:  A2EG54
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S10p/S20e, putativeV [auth U]123Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_086300
Find proteins for A2FDE0 (Trichomonas vaginalis)
Explore A2FDE0 
Go to UniProtKB:  A2FDE0
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S21W [auth V]89Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_022100
Find proteins for A2FFS8 (Trichomonas vaginalis)
Explore A2FFS8 
Go to UniProtKB:  A2FFS8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S15aX [auth W]130Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_006250TVAG_462530
Find proteins for A2DLW4 (Trichomonas vaginalis)
Explore A2DLW4 
Go to UniProtKB:  A2DLW4
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S23, putativeY [auth X]144Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_071920TVAG_109530TVAG_109730TVAG_159830TVAG_198620TVAG_249090TVAG_305300TVAG_430260
Find proteins for A2D895 (Trichomonas vaginalis)
Explore A2D895 
Go to UniProtKB:  A2D895
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S24e, putativeZ [auth Y]140Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_272960TVAG_272970TVAG_272980TVAG_386300
Find proteins for A2F0H5 (Trichomonas vaginalis)
Explore A2F0H5 
Go to UniProtKB:  A2F0H5
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinAA [auth Z]115Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_226630
Find proteins for A2ER97 (Trichomonas vaginalis)
Explore A2ER97 
Go to UniProtKB:  A2ER97
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S26BA [auth a]118Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_040120TVAG_061920TVAG_164600TVAG_242190TVAG_277940TVAG_302160TVAG_333200TVAG_335820TVAG_347960
Find proteins for A2DST7 (Trichomonas vaginalis)
Explore A2DST7 
Go to UniProtKB:  A2DST7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S27CA [auth b]86Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_064320
Find proteins for A2FBZ2 (Trichomonas vaginalis)
Explore A2FBZ2 
Go to UniProtKB:  A2FBZ2
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinDA [auth c]68Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_050990TVAG_057380TVAG_266850TVAG_272940TVAG_272950TVAG_327180
Find proteins for A2DQN8 (Trichomonas vaginalis)
Explore A2DQN8 
Go to UniProtKB:  A2DQN8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S29, putativeEA [auth d]57Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_107660TVAG_131520TVAG_357220TVAG_366620TVAG_393120TVAG_490210
Find proteins for A2DYA8 (Trichomonas vaginalis)
Explore A2DYA8 
Go to UniProtKB:  A2DYA8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S30FA [auth e]62Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_222910
Find proteins for A2FHY5 (Trichomonas vaginalis)
Explore A2FHY5 
Go to UniProtKB:  A2FHY5
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein beta subunit, putativeGA [auth g]335Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_151920
Find proteins for A2ELV7 (Trichomonas vaginalis)
Explore A2ELV7 
Go to UniProtKB:  A2ELV7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
eL41HA [auth n]25Trichomonas vaginalisMutation(s): 0 
Find proteins for P0CX86 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX86 
Go to UniProtKB:  P0CX86
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
18SA [auth 2]1577Trichomonas vaginalis
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.35 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: 2017-10-18
    Changes: Database references