5XXU

Small subunit of Toxoplasma gondii 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 1.2 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 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

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein uS2A287Toxoplasma gondiiMutation(s): 0 
Find proteins for Q8MPF7 (Toxoplasma gondii)
Explore Q8MPF7 
Go to UniProtKB:  Q8MPF7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein eS1B259Toxoplasma gondiiMutation(s): 0 
Find proteins for B9PGG2 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore B9PGG2 
Go to UniProtKB:  B9PGG2
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein uS5C269Toxoplasma gondiiMutation(s): 0 
Find proteins for B9PZF2 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore B9PZF2 
Go to UniProtKB:  B9PZF2
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein uS3D235Toxoplasma gondiiMutation(s): 0 
Find proteins for A0A0F7UXI8 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore A0A0F7UXI8 
Go to UniProtKB:  A0A0F7UXI8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein eS4E263Toxoplasma gondiiMutation(s): 0 
Gene Names: TgIb.0120c
Find proteins for Q1JSZ0 (Toxoplasma gondii)
Explore Q1JSZ0 
Go to UniProtKB:  Q1JSZ0
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein uS7F192Toxoplasma gondiiMutation(s): 0 
Find proteins for B9PPE8 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore B9PPE8 
Go to UniProtKB:  B9PPE8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein eS6G256Toxoplasma gondiiMutation(s): 0 
Find proteins for B9PVR5 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore B9PVR5 
Go to UniProtKB:  B9PVR5
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein eS7H196Toxoplasma gondiiMutation(s): 0 
Find proteins for B9PNL1 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore B9PNL1 
Go to UniProtKB:  B9PNL1
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein eS8I205Toxoplasma gondiiMutation(s): 0 
Find proteins for B6KGK3 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore B6KGK3 
Go to UniProtKB:  B6KGK3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein uS4J188Toxoplasma gondiiMutation(s): 0 
Find proteins for B9PQU8 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore B9PQU8 
Go to UniProtKB:  B9PQU8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein eS10K152Toxoplasma gondiiMutation(s): 0 
Find proteins for B9PX63 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore B9PX63 
Go to UniProtKB:  B9PX63
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein uS17L161Toxoplasma gondiiMutation(s): 0 
Find proteins for B9PMU7 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore B9PMU7 
Go to UniProtKB:  B9PMU7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein eS12M142Toxoplasma gondiiMutation(s): 0 
Find proteins for B9Q056 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore B9Q056 
Go to UniProtKB:  B9Q056
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein uS15N151Toxoplasma gondiiMutation(s): 0 
Find proteins for A0A125YSG6 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore A0A125YSG6 
Go to UniProtKB:  A0A125YSG6
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein uS11O156Toxoplasma gondiiMutation(s): 0 
Find proteins for A0A125YXW4 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore A0A125YXW4 
Go to UniProtKB:  A0A125YXW4
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein uS19P150Toxoplasma gondiiMutation(s): 0 
Find proteins for B9PSN8 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore B9PSN8 
Go to UniProtKB:  B9PSN8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein uS9Q148Toxoplasma gondiiMutation(s): 0 
Find proteins for B6KC70 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore B6KC70 
Go to UniProtKB:  B6KC70
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein eS17R132Toxoplasma gondiiMutation(s): 0 
Gene Names: TgIb.0420c
Find proteins for B9PXH2 (Toxoplasma gondii)
Explore B9PXH2 
Go to UniProtKB:  B9PXH2
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein uS13S156Toxoplasma gondiiMutation(s): 0 
Find proteins for B9PMB3 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore B9PMB3 
Go to UniProtKB:  B9PMB3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein eS19T160Toxoplasma gondiiMutation(s): 0 
Find proteins for A0A125YMR9 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore A0A125YMR9 
Go to UniProtKB:  A0A125YMR9
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein uS10U233Toxoplasma gondiiMutation(s): 0 
Find proteins for B6KQG9 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore B6KQG9 
Go to UniProtKB:  B6KQG9
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein eS21V82Toxoplasma gondiiMutation(s): 0 
Find proteins for A0A125YS47 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore A0A125YS47 
Go to UniProtKB:  A0A125YS47
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein uS8W130Toxoplasma gondiiMutation(s): 0 
Find proteins for A0A125YJX3 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore A0A125YJX3 
Go to UniProtKB:  A0A125YJX3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein uS12X143Toxoplasma gondiiMutation(s): 0 
Find proteins for B9PHL8 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore B9PHL8 
Go to UniProtKB:  B9PHL8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein eS24Y135Toxoplasma gondiiMutation(s): 0 
Find proteins for A0A125YKH1 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore A0A125YKH1 
Go to UniProtKB:  A0A125YKH1
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein eS25Z161Toxoplasma gondiiMutation(s): 0 
Find proteins for S7V273 (Toxoplasma gondii (strain ATCC 50853 / GT1))
Explore S7V273 
Go to UniProtKB:  S7V273
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein eS26a112Toxoplasma gondiiMutation(s): 0 
Find proteins for B9PP49 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore B9PP49 
Go to UniProtKB:  B9PP49
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein eS27b82Toxoplasma gondiiMutation(s): 0 
Find proteins for A0A125YVX8 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore A0A125YVX8 
Go to UniProtKB:  A0A125YVX8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein eS28c68Toxoplasma gondiiMutation(s): 0 
Find proteins for A0A125YJ29 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore A0A125YJ29 
Go to UniProtKB:  A0A125YJ29
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein uS14d54Toxoplasma gondiiMutation(s): 0 
Find proteins for A0A0F7UYM7 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore A0A0F7UYM7 
Go to UniProtKB:  A0A0F7UYM7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein eS30e59Toxoplasma gondiiMutation(s): 0 
Find proteins for B9PTA0 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore B9PTA0 
Go to UniProtKB:  B9PTA0
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein eS31f154Toxoplasma gondiiMutation(s): 0 
Find proteins for B9PQ37 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Explore B9PQ37 
Go to UniProtKB:  B9PQ37
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein eL41m39Toxoplasma gondiiMutation(s): 0 
Find proteins for F0JB24 (Neospora caninum (strain Liverpool))
Explore F0JB24 
Go to UniProtKB:  F0JB24
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
18S RNA21791Toxoplasma gondii
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 

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2017-10-18
    Changes: Database references
  • Version 1.2: 2018-10-24
    Changes: Data collection, Refinement description