5XXB

Large subunit of Toxoplasma gondii ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.17 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL2
A
260Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL3
B
389Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL4
C
416Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL30
F
258Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL6
H
190Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL16
I
221Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL5
J
175Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL13
K
355Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL14
L
134Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL15
M
205Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL18
P
187Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL19
Q
187Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL20
R
183Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL21
S
157Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL22
T
133Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL14
U
139Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL24
V
155Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL27
Y
146Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL15
Z
147Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL31
c
120Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL33
e
112Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL29
g
123Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL37
i
98Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL38
j
84Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL39
k
51Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL40
l
129Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL43
o
96Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL8
G
276Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL13
N
269Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL22
O
195Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL23
W
167Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL24
X
141Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL29
a
54Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL30
b
108Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL32
d
134Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL34
f
134Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL36
h
101Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL42
n
105Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL28
p
129Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein uL18
D
310Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein eL6
E
193Toxoplasma gondiiMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence   |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
25S RNA13477Toxoplasma gondii

Find similar proteins by: Sequence   |  Structure

Entity ID: 3
MoleculeChainsLengthOrganism
5.8S RNA4158Toxoplasma gondii

Find similar proteins by: Sequence   |  Structure

Entity ID: 2
MoleculeChainsLengthOrganism
5S RNA3124Toxoplasma gondii
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.17 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