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:  

  • 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.,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China.,Center for Parasitic Organisms, State Key Laboratory of Biocontrol, Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510275, China.,State Key Laboratory of Agrobiotechnology &National Animal Protozoa Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.,State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Anhui Provincial Laboratory of Pathogen Biology, Anhui Key Laboratory of Zoonoses, Department of Microbiology and Parasitology, Anhui Medical University, Hefei, Anhui 230022, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uS2
A
287Toxoplasma gondiiMutation(s): 0 
Find proteins for Q8MPF7 (Toxoplasma gondii)
Go to UniProtKB:  Q8MPF7
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eS1
B
259Toxoplasma gondii (strain ATCC 50861 / VEG)Mutation(s): 0 
Find proteins for B9PGG2 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Go to UniProtKB:  B9PGG2
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uS5
C
269Toxoplasma gondii (strain ATCC 50861 / VEG)Mutation(s): 0 
Find proteins for B9PZF2 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Go to UniProtKB:  B9PZF2
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uS3
D
235Toxoplasma gondii (strain ATCC 50861 / VEG)Mutation(s): 0 
Find proteins for A0A0F7UXI8 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Go to UniProtKB:  A0A0F7UXI8
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eS4
E
263Toxoplasma gondiiMutation(s): 0 
Find proteins for Q1JSZ0 (Toxoplasma gondii)
Go to UniProtKB:  Q1JSZ0
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uS7
F
192Toxoplasma gondii (strain ATCC 50861 / VEG)Mutation(s): 0 
Find proteins for B9PPE8 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Go to UniProtKB:  B9PPE8
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eS6
G
256Toxoplasma gondii (strain ATCC 50861 / VEG)Mutation(s): 0 
Find proteins for B9PVR5 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Go to UniProtKB:  B9PVR5
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eS7
H
196Toxoplasma gondii (strain ATCC 50861 / VEG)Mutation(s): 0 
Find proteins for B9PNL1 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Go to UniProtKB:  B9PNL1
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eS8
I
205Toxoplasma gondii (strain ATCC 50861 / VEG)Mutation(s): 0 
Find proteins for B6KGK3 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Go to UniProtKB:  B6KGK3
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uS4
J
188Toxoplasma gondii (strain ATCC 50861 / VEG)Mutation(s): 0 
Find proteins for B9PQU8 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Go to UniProtKB:  B9PQU8
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eS10
K
152Toxoplasma gondii (strain ATCC 50861 / VEG)Mutation(s): 0 
Find proteins for B9PX63 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Go to UniProtKB:  B9PX63
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uS17
L
161Toxoplasma gondii (strain ATCC 50861 / VEG)Mutation(s): 0 
Find proteins for B9PMU7 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Go to UniProtKB:  B9PMU7
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eS12
M
142Toxoplasma gondii (strain ATCC 50861 / VEG)Mutation(s): 0 
Find proteins for B9Q056 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Go to UniProtKB:  B9Q056
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uS15
N
151Toxoplasma gondii (strain ATCC 50861 / VEG)Mutation(s): 0 
Find proteins for A0A125YSG6 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Go to UniProtKB:  A0A125YSG6
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uS11
O
156Toxoplasma gondii (strain ATCC 50861 / VEG)Mutation(s): 0 
Find proteins for A0A125YXW4 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Go to UniProtKB:  A0A125YXW4
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uS19
P
150Toxoplasma gondii (strain ATCC 50861 / VEG)Mutation(s): 0 
Find proteins for B9PSN8 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Go to UniProtKB:  B9PSN8
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uS9
Q
148Toxoplasma gondii (strain ATCC 50861 / VEG)Mutation(s): 0 
Find proteins for B6KC70 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Go to UniProtKB:  B6KC70
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eS17
R
132Toxoplasma gondiiMutation(s): 0 
Find proteins for B9PXH2 (Toxoplasma gondii)
Go to UniProtKB:  B9PXH2
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uS13
S
156Toxoplasma gondii (strain ATCC 50861 / VEG)Mutation(s): 0 
Find proteins for B9PMB3 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Go to UniProtKB:  B9PMB3
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eS19
T
160Toxoplasma gondii (strain ATCC 50861 / VEG)Mutation(s): 0 
Find proteins for A0A125YMR9 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Go to UniProtKB:  A0A125YMR9
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uS10
U
233Toxoplasma gondii (strain ATCC 50861 / VEG)Mutation(s): 0 
Find proteins for B6KQG9 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Go to UniProtKB:  B6KQG9
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eS21
V
82Toxoplasma gondii (strain ATCC 50861 / VEG)Mutation(s): 0 
Find proteins for A0A125YS47 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Go to UniProtKB:  A0A125YS47
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uS8
W
130Toxoplasma gondii (strain ATCC 50861 / VEG)Mutation(s): 0 
Find proteins for A0A125YJX3 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Go to UniProtKB:  A0A125YJX3
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uS12
X
143Toxoplasma gondii (strain ATCC 50861 / VEG)Mutation(s): 0 
Find proteins for B9PHL8 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Go to UniProtKB:  B9PHL8
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eS24
Y
135Toxoplasma gondii (strain ATCC 50861 / VEG)Mutation(s): 0 
Find proteins for A0A125YKH1 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Go to UniProtKB:  A0A125YKH1
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eS25
Z
161Toxoplasma gondii (strain ATCC 50853 / GT1)Mutation(s): 0 
Find proteins for S7V273 (Toxoplasma gondii (strain ATCC 50853 / GT1))
Go to UniProtKB:  S7V273
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eS26
a
112Toxoplasma gondii (strain ATCC 50861 / VEG)Mutation(s): 0 
Find proteins for B9PP49 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Go to UniProtKB:  B9PP49
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eS27
b
82Toxoplasma gondii (strain ATCC 50861 / VEG)Mutation(s): 0 
Find proteins for A0A125YVX8 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Go to UniProtKB:  A0A125YVX8
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eS28
c
68Toxoplasma gondii (strain ATCC 50861 / VEG)Mutation(s): 0 
Find proteins for A0A125YJ29 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Go to UniProtKB:  A0A125YJ29
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uS14
d
54Toxoplasma gondii (strain ATCC 50861 / VEG)Mutation(s): 0 
Find proteins for A0A0F7UYM7 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Go to UniProtKB:  A0A0F7UYM7
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eS30
e
59Toxoplasma gondii (strain ATCC 50861 / VEG)Mutation(s): 0 
Find proteins for B9PTA0 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Go to UniProtKB:  B9PTA0
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eS31
f
154Toxoplasma gondii (strain ATCC 50861 / VEG)Mutation(s): 0 
Find proteins for B9PQ37 (Toxoplasma gondii (strain ATCC 50861 / VEG))
Go to UniProtKB:  B9PQ37
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL41
m
39Neospora caninum (strain Liverpool)Mutation(s): 0 
Find proteins for F0JB24 (Neospora caninum (strain Liverpool))
Go to UniProtKB:  F0JB24
Entity ID: 1
MoleculeChainsLengthOrganism
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 or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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