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:  

  • 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: 2
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein SA
A
256Trichomonas vaginalisMutation(s): 0 
Find proteins for A2EFE7 (Trichomonas vaginalis)
Go to UniProtKB:  A2EFE7
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S3Ae, putative
B
247Trichomonas vaginalisMutation(s): 0 
Find proteins for A2G9Z8 (Trichomonas vaginalis)
Go to UniProtKB:  A2G9Z8
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
C
272Trichomonas vaginalisMutation(s): 0 
Find proteins for A2EHK3 (Trichomonas vaginalis)
Go to UniProtKB:  A2EHK3
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S3, putative
D
216Trichomonas vaginalisMutation(s): 0 
Find proteins for A2DIM3 (Trichomonas vaginalis)
Go to UniProtKB:  A2DIM3
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4
E
255Trichomonas vaginalisMutation(s): 0 
Find proteins for A2FC75 (Trichomonas vaginalis)
Go to UniProtKB:  A2FC75
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
40s ribosomal protein S5-B, putative
F
193Trichomonas vaginalisMutation(s): 0 
Find proteins for A2E4S6 (Trichomonas vaginalis)
Go to UniProtKB:  A2E4S6
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S6
G
216Trichomonas vaginalisMutation(s): 0 
Find proteins for A2DEJ9 (Trichomonas vaginalis)
Go to UniProtKB:  A2DEJ9
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S7, putative
H
168Trichomonas vaginalisMutation(s): 0 
Find proteins for A2G5X6 (Trichomonas vaginalis)
Go to UniProtKB:  A2G5X6
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S8
I
197Trichomonas vaginalisMutation(s): 0 
Find proteins for A2E1L5 (Trichomonas vaginalis)
Go to UniProtKB:  A2E1L5
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
J
185Trichomonas vaginalisMutation(s): 0 
Find proteins for A2DNY3 (Trichomonas vaginalis)
Go to UniProtKB:  A2DNY3
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Plectin/S10 domain containing protein
K
141Trichomonas vaginalisMutation(s): 0 
Find proteins for A2EBA2 (Trichomonas vaginalis)
Go to UniProtKB:  A2EBA2
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
L
155Trichomonas vaginalisMutation(s): 0 
Find proteins for A2DHU8 (Trichomonas vaginalis)
Go to UniProtKB:  A2DHU8
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L7Ae, putative
M
124Trichomonas vaginalisMutation(s): 0 
Find proteins for A2FA40 (Trichomonas vaginalis)
Go to UniProtKB:  A2FA40
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13, putative
N
151Trichomonas vaginalisMutation(s): 0 
Find proteins for A2D9L2 (Trichomonas vaginalis)
Go to UniProtKB:  A2D9L2
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S14
O
159Trichomonas vaginalisMutation(s): 0 
Find proteins for Q76KS8 (Trichomonas vaginalis)
Go to UniProtKB:  Q76KS8
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S19, putative
P
144Trichomonas vaginalisMutation(s): 0 
Find proteins for A2DVD8 (Trichomonas vaginalis)
Go to UniProtKB:  A2DVD8
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16, putative
Q
140Trichomonas vaginalisMutation(s): 0 
Find proteins for A2D919 (Trichomonas vaginalis)
Go to UniProtKB:  A2D919
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S17-B, putative
R
129Trichomonas vaginalisMutation(s): 0 
Find proteins for A2DPS3 (Trichomonas vaginalis)
Go to UniProtKB:  A2DPS3
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S13p/S18e, putative
S
155Trichomonas vaginalisMutation(s): 0 
Find proteins for A2DTR8 (Trichomonas vaginalis)
Go to UniProtKB:  A2DTR8
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S19e, putative
T
148Trichomonas vaginalisMutation(s): 0 
Find proteins for A2EG54 (Trichomonas vaginalis)
Go to UniProtKB:  A2EG54
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S10p/S20e, putative
U
123Trichomonas vaginalisMutation(s): 0 
Find proteins for A2FDE0 (Trichomonas vaginalis)
Go to UniProtKB:  A2FDE0
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S21
V
89Trichomonas vaginalisMutation(s): 0 
Find proteins for A2FFS8 (Trichomonas vaginalis)
Go to UniProtKB:  A2FFS8
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S15a
W
130Trichomonas vaginalisMutation(s): 0 
Find proteins for A2DLW4 (Trichomonas vaginalis)
Go to UniProtKB:  A2DLW4
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23, putative
X
144Trichomonas vaginalisMutation(s): 0 
Find proteins for A2D895 (Trichomonas vaginalis)
Go to UniProtKB:  A2D895
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S24e, putative
Y
140Trichomonas vaginalisMutation(s): 0 
Find proteins for A2F0H5 (Trichomonas vaginalis)
Go to UniProtKB:  A2F0H5
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
Z
115Trichomonas vaginalisMutation(s): 0 
Find proteins for A2ER97 (Trichomonas vaginalis)
Go to UniProtKB:  A2ER97
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S26
a
118Trichomonas vaginalisMutation(s): 0 
Find proteins for A2DST7 (Trichomonas vaginalis)
Go to UniProtKB:  A2DST7
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27
b
86Trichomonas vaginalisMutation(s): 0 
Find proteins for A2FBZ2 (Trichomonas vaginalis)
Go to UniProtKB:  A2FBZ2
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
c
68Trichomonas vaginalisMutation(s): 0 
Find proteins for A2DQN8 (Trichomonas vaginalis)
Go to UniProtKB:  A2DQN8
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S29, putative
d
57Trichomonas vaginalisMutation(s): 0 
Find proteins for A2DYA8 (Trichomonas vaginalis)
Go to UniProtKB:  A2DYA8
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S30
e
62Trichomonas vaginalisMutation(s): 0 
Find proteins for A2FHY5 (Trichomonas vaginalis)
Go to UniProtKB:  A2FHY5
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein beta subunit, putative
g
335Trichomonas vaginalisMutation(s): 0 
Find proteins for A2ELV7 (Trichomonas vaginalis)
Go to UniProtKB:  A2ELV7
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
eL41
n
25Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL41A (RPL47A, YL41A)
Find proteins for P0CX86 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX86
Entity ID: 1
MoleculeChainsLengthOrganism
18S21577Trichomonas vaginalis
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