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- PDB-5xxb: Large subunit of Toxoplasma gondii ribosome -

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Basic information

Entry
Database: PDB / ID: 5xxb
TitleLarge subunit of Toxoplasma gondii ribosome
Components
  • (Ribosomal protein ...) x 41
  • 25S RNA
  • 5.8S RNA
  • 5S RNA
KeywordsRIBOSOME / parasitic ribosome / rRNA / rproteins
Function / homologyRNA / RNA (> 10) / RNA (> 100) / RNA (> 1000)
Function and homology information
Biological speciesToxoplasma gondii (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsLi, Z. / Guo, Q. / Zheng, L. / Ji, Y. / Xie, Y. / Lai, D. / Lun, Z. / Suo, X. / Gao, N.
CitationJournal: Cell Res / Year: 2017
Title: Cryo-EM structures of the 80S ribosomes from human parasites Trichomonas vaginalis and Toxoplasma gondii.
Authors: Zhifei Li / Qiang Guo / Lvqin Zheng / Yongsheng Ji / Yi-Ting Xie / De-Hua Lai / Zhao-Rong Lun / Xun Suo / Ning Gao /
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- ...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.
History
DepositionJul 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Assembly

Deposited unit
1: 25S RNA
3: 5S RNA
4: 5.8S RNA
A: Ribosomal protein uL2
B: Ribosomal protein uL3
C: Ribosomal protein uL4
D: Ribosomal protein uL18
E: Ribosomal protein eL6
F: Ribosomal protein uL30
G: Ribosomal protein eL8
H: Ribosomal protein uL6
I: Ribosomal protein uL16
J: Ribosomal protein uL5
K: Ribosomal protein eL13
L: Ribosomal protein eL14
M: Ribosomal protein eL15
N: Ribosomal protein uL13
O: Ribosomal protein uL22
P: Ribosomal protein eL18
Q: Ribosomal protein eL19
R: Ribosomal protein eL20
S: Ribosomal protein eL21
T: Ribosomal protein eL22
U: Ribosomal protein uL14
V: Ribosomal protein eL24
W: Ribosomal protein uL23
X: Ribosomal protein uL24
Y: Ribosomal protein eL27
Z: Ribosomal protein uL15
a: Ribosomal protein eL29
b: Ribosomal protein eL30
c: Ribosomal protein eL31
d: Ribosomal protein eL32
e: Ribosomal protein eL33
f: Ribosomal protein eL34
g: Ribosomal protein uL29
h: Ribosomal protein eL36
i: Ribosomal protein eL37
j: Ribosomal protein eL38
k: Ribosomal protein eL39
l: Ribosomal protein eL40
n: Ribosomal protein eL42
o: Ribosomal protein eL43
p: Ribosomal protein eL28


Theoretical massNumber of molelcules
Total (without water)2,027,34644
Polymers2,027,34644
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area361790 Å2
ΔGint-3074 kcal/mol
Surface area621290 Å2

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Components

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RNA chain , 3 types, 3 molecules 134

#1: RNA chain 25S RNA


Mass: 1120153.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#2: RNA chain 5S RNA


Mass: 39921.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#3: RNA chain 5.8S RNA


Mass: 50787.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)

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Ribosomal protein ... , 41 types, 41 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZabcd...

#4: Protein Ribosomal protein uL2


Mass: 28314.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#5: Protein Ribosomal protein uL3


Mass: 44150.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#6: Protein Ribosomal protein uL4


Mass: 45837.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#7: Protein Ribosomal protein uL18


Mass: 35408.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#8: Protein Ribosomal protein eL6


Mass: 21563.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#9: Protein Ribosomal protein uL30


Mass: 30187.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#10: Protein Ribosomal protein eL8


Mass: 31095.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#11: Protein Ribosomal protein uL6


Mass: 21459.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#12: Protein Ribosomal protein uL16


Mass: 24846.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#13: Protein Ribosomal protein uL5


Mass: 20240.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#14: Protein Ribosomal protein eL13


Mass: 39757.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#15: Protein Ribosomal protein eL14


Mass: 15492.432 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#16: Protein Ribosomal protein eL15


Mass: 24387.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#17: Protein Ribosomal protein uL13


Mass: 31757.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#18: Protein Ribosomal protein uL22


Mass: 22319.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#19: Protein Ribosomal protein eL18


Mass: 21223.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#20: Protein Ribosomal protein eL19


Mass: 22221.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#21: Protein Ribosomal protein eL20


Mass: 21372.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#22: Protein Ribosomal protein eL21


Mass: 17932.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#23: Protein Ribosomal protein eL22


Mass: 15103.659 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#24: Protein Ribosomal protein uL14


Mass: 14842.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#25: Protein Ribosomal protein eL24


Mass: 17644.857 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#26: Protein Ribosomal protein uL23


Mass: 18600.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#27: Protein Ribosomal protein uL24


Mass: 16353.228 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#28: Protein Ribosomal protein eL27


Mass: 16841.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#29: Protein Ribosomal protein uL15


Mass: 16384.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#30: Protein Ribosomal protein eL29


Mass: 6387.679 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#31: Protein Ribosomal protein eL30


Mass: 11682.658 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#32: Protein Ribosomal protein eL31


Mass: 14389.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#33: Protein Ribosomal protein eL32


Mass: 15652.334 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#34: Protein Ribosomal protein eL33


Mass: 12873.091 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#35: Protein Ribosomal protein eL34


Mass: 15427.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#36: Protein Ribosomal protein uL29


Mass: 14231.108 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#37: Protein Ribosomal protein eL36


Mass: 11437.687 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#38: Protein Ribosomal protein eL37


Mass: 11256.210 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#39: Protein Ribosomal protein eL38


Mass: 9606.386 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#40: Protein Ribosomal protein eL39


Mass: 6172.519 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#41: Protein Ribosomal protein eL40


Mass: 14714.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#42: Protein Ribosomal protein eL42


Mass: 12098.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#43: Protein Ribosomal protein eL43


Mass: 10426.384 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)
#44: Protein Ribosomal protein eL28


Mass: 14787.717 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)

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Details

Has protein modificationY
Sequence detailsSequences used in this study were derived from Toxoplasma gondii RH strain, which were not ...Sequences used in this study were derived from Toxoplasma gondii RH strain, which were not available at UNIPROT at the time of data processing.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Large subunit of Toxoplasma gondii ribosome / Type: RIBOSOME / Entity ID: all / Source: NATURAL
Source (natural)Organism: Toxoplasma gondii (eukaryote)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 108162 / Symmetry type: POINT

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