5XY3

Large subunit of Trichomonas vaginalis ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.2 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, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L8, putative
A
251Trichomonas vaginalisMutation(s): 0 
Find proteins for A2E6Z8 (Trichomonas vaginalis)
Go to UniProtKB:  A2E6Z8
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
B
415Trichomonas vaginalisMutation(s): 0 
Find proteins for A2DD62 (Trichomonas vaginalis)
Go to UniProtKB:  A2DD62
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein, putative
C
370Trichomonas vaginalisMutation(s): 0 
Find proteins for A2E4D0 (Trichomonas vaginalis)
Go to UniProtKB:  A2E4D0
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L5
D
308Trichomonas vaginalisMutation(s): 0 
Find proteins for A2DNM5 (Trichomonas vaginalis)
Go to UniProtKB:  A2DNM5
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6, putative
E
151Trichomonas vaginalisMutation(s): 0 
Find proteins for A2FXW1 (Trichomonas vaginalis)
Go to UniProtKB:  A2FXW1
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L30p/L7e, putative
F
239Trichomonas vaginalisMutation(s): 0 
Find proteins for A2F592 (Trichomonas vaginalis)
Go to UniProtKB:  A2F592
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L7Ae, putative
G
244Trichomonas vaginalisMutation(s): 0 
Find proteins for A2ET60 (Trichomonas vaginalis)
Go to UniProtKB:  A2ET60
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L6, putative
H
197Trichomonas vaginalisMutation(s): 0 
Find proteins for A2DDT1 (Trichomonas vaginalis)
Go to UniProtKB:  A2DDT1
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein, putative
I
209Trichomonas vaginalisMutation(s): 0 
Find proteins for A2FVZ6 (Trichomonas vaginalis)
Go to UniProtKB:  A2FVZ6
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11, putative
J
169Trichomonas vaginalisMutation(s): 0 
Find proteins for A2E7L8 (Trichomonas vaginalis)
Go to UniProtKB:  A2E7L8
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L13e, putative
L
189Trichomonas vaginalisMutation(s): 0 
Find proteins for A2G4E1 (Trichomonas vaginalis)
Go to UniProtKB:  A2G4E1
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L14, putative
M
128Trichomonas vaginalisMutation(s): 0 
Find proteins for A2DZ49 (Trichomonas vaginalis)
Go to UniProtKB:  A2DZ49
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L15
N
204Trichomonas vaginalisMutation(s): 0 
Find proteins for A2ECR7 (Trichomonas vaginalis)
Go to UniProtKB:  A2ECR7
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L13, putative
O
200Trichomonas vaginalisMutation(s): 0 
Find proteins for A2DZ26 (Trichomonas vaginalis)
Go to UniProtKB:  A2DZ26
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L22, putative
P
164Trichomonas vaginalisMutation(s): 0 
Find proteins for A2DM53 (Trichomonas vaginalis)
Go to UniProtKB:  A2DM53
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18, putative
Q
186Trichomonas vaginalisMutation(s): 0 
Find proteins for A2D7Q5 (Trichomonas vaginalis)
Go to UniProtKB:  A2D7Q5
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19-3, putative
R
178Trichomonas vaginalisMutation(s): 0 
Find proteins for A2D8G1 (Trichomonas vaginalis)
Go to UniProtKB:  A2D8G1
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18a
S
176Trichomonas vaginalisMutation(s): 0 
Find proteins for A2EP03 (Trichomonas vaginalis)
Go to UniProtKB:  A2EP03
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L21e, putative
T
159Trichomonas vaginalisMutation(s): 0 
Find proteins for A2F2S5 (Trichomonas vaginalis)
Go to UniProtKB:  A2F2S5
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L22-1, putative
U
106Trichomonas vaginalisMutation(s): 0 
Find proteins for A2DNV5 (Trichomonas vaginalis)
Go to UniProtKB:  A2DNV5
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23, putative
V
140Trichomonas vaginalisMutation(s): 0 
Find proteins for A2DP51 (Trichomonas vaginalis)
Go to UniProtKB:  A2DP51
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L24e, putative
W
113Trichomonas vaginalisMutation(s): 0 
Find proteins for A2DJQ1 (Trichomonas vaginalis)
Go to UniProtKB:  A2DJQ1
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L23, putative
X
140Trichomonas vaginalisMutation(s): 0 
Find proteins for A2DUV8 (Trichomonas vaginalis)
Go to UniProtKB:  A2DUV8
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L24, putative
Y
138Trichomonas vaginalisMutation(s): 0 
Find proteins for A2DKF2 (Trichomonas vaginalis)
Go to UniProtKB:  A2DKF2
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L27e, putative
Z
139Trichomonas vaginalisMutation(s): 0 
Find proteins for A2DNC1 (Trichomonas vaginalis)
Go to UniProtKB:  A2DNC1
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
a
151Trichomonas vaginalisMutation(s): 0 
Find proteins for A2DHU7 (Trichomonas vaginalis)
Go to UniProtKB:  A2DHU7
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29
b
58Trichomonas vaginalisMutation(s): 0 
Find proteins for A2DM33 (Trichomonas vaginalis)
Go to UniProtKB:  A2DM33
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30, putative
c
112Trichomonas vaginalisMutation(s): 0 
Find proteins for A2E6Z9 (Trichomonas vaginalis)
Go to UniProtKB:  A2E6Z9
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L31e, putative
d
110Trichomonas vaginalisMutation(s): 0 
Find proteins for A2D9N8 (Trichomonas vaginalis)
Go to UniProtKB:  A2D9N8
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L32, putative
e
132Trichomonas vaginalisMutation(s): 0 
Find proteins for A2F2J0 (Trichomonas vaginalis)
Go to UniProtKB:  A2F2J0
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L35Ae, putative
f
102Trichomonas vaginalisMutation(s): 0 
Find proteins for A2DSF3 (Trichomonas vaginalis)
Go to UniProtKB:  A2DSF3
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L34e, putative
g
116Trichomonas vaginalisMutation(s): 0 
Find proteins for A2FWA1 (Trichomonas vaginalis)
Go to UniProtKB:  A2FWA1
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L29, putative
h
124Trichomonas vaginalisMutation(s): 0 
Find proteins for A2E6R2 (Trichomonas vaginalis)
Go to UniProtKB:  A2E6R2
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L36e, putative
i
91Trichomonas vaginalisMutation(s): 0 
Find proteins for A2EXW7 (Trichomonas vaginalis)
Go to UniProtKB:  A2EXW7
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L37
j
81Trichomonas vaginalisMutation(s): 0 
Find proteins for A2F8Y8 (Trichomonas vaginalis)
Go to UniProtKB:  A2F8Y8
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L38e, putative
k
74Trichomonas vaginalisMutation(s): 0 
Find proteins for A2FFH9 (Trichomonas vaginalis)
Go to UniProtKB:  A2FFH9
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L39, putative
l
51Trichomonas vaginalisMutation(s): 0 
Find proteins for A2D9N4 (Trichomonas vaginalis)
Go to UniProtKB:  A2D9N4
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin, putative
m
132Trichomonas vaginalisMutation(s): 0 
Find proteins for A2DGL5 (Trichomonas vaginalis)
Go to UniProtKB:  A2DGL5
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L44, putative
o
104Trichomonas vaginalisMutation(s): 0 
Find proteins for A2DAI6 (Trichomonas vaginalis)
Go to UniProtKB:  A2DAI6
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
p
92Trichomonas vaginalisMutation(s): 0 
Find proteins for A2DEM7 (Trichomonas vaginalis)
Go to UniProtKB:  A2DEM7
Entity ID: 1
MoleculeChainsLengthOrganism
25S ribosomal RNA12765Trichomonas vaginalis
Entity ID: 2
MoleculeChainsLengthOrganism
5S ribosomal RNA3118Trichomonas vaginalis
Entity ID: 3
MoleculeChainsLengthOrganism
5.8S ribosomal RNA4162Trichomonas vaginalis
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.2 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: 2017-09-06
    Type: Structure summary
  • Version 1.2: 2017-10-18
    Type: Database references