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- PDB-5xxu: Small subunit of Toxoplasma gondii ribosome -

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Basic information

Entry
Database: PDB / ID: 5xxu
TitleSmall subunit of Toxoplasma gondii ribosome
Components
  • (Ribosomal protein ...) x 33
  • 18S RNA
KeywordsRIBOSOME / Toxoplasma gondii ribosome / rRNA / rprotein
Function / homology
Function and homology information


ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / ribosome / rRNA binding / structural constituent of ribosome / translation / RNA binding / zinc ion binding / integral component of membrane
Ribosomal protein S28e conserved site / Winged helix-like DNA-binding domain superfamily / S25 ribosomal protein / 50S ribosomal protein L30e-like / Ubiquitin-like domain superfamily / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / Ribosomal protein S8 superfamily / Winged helix DNA-binding domain superfamily / 40S ribosomal protein S1/3, eukaryotes ...Ribosomal protein S28e conserved site / Winged helix-like DNA-binding domain superfamily / S25 ribosomal protein / 50S ribosomal protein L30e-like / Ubiquitin-like domain superfamily / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / Ribosomal protein S8 superfamily / Winged helix DNA-binding domain superfamily / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S17e-like superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S11 superfamily / RNA-binding S4 domain superfamily / 40S Ribosomal protein S10 / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S2, eukaryotic / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S7, conserved site / Ribosomal protein S21e, conserved site / Ribosomal protein S6e, conserved site / Ubiquitin domain / Ribosomal protein S17, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein S10 domain / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S4/S9 / Ribosomal protein S15P / Ribosomal protein S19, superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S7 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein S19e domain superfamily / Ribosomal protein S26e superfamily / Ribosomal S3Ae family / 40S ribosomal protein S4 C-terminus / Plectin/S10 domain / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S8e / Ribosomal protein S7e / Ribosomal protein S6e / Ribosomal protein S7p/S5e / RS4NT (NUC023) domain / Ribosomal_S17 N-terminal / S4 domain / Ribosomal family S4e / KOW motif / KH domain / Ribosomal protein S3, C-terminal domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S5, N-terminal domain / Ribosomal protein S17 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein S21e superfamily / Ribosomal protein S21e / S27a-like superfamily / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S4, KOW domain / Ribosomal protein S24e / Ribosomal protein S12/S23 / Ribosomal protein S8 / Ribosomal protein S10p/S20e / Ribosomal protein S15 / Ribosomal protein S19e / Ribosomal protein S13/S18 / Ribosomal S17 / Ribosomal protein S9/S16 / Ribosomal protein S19 / Ribosomal protein S11 / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S17e, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S3, C-terminal / Ribosomal protein S4e / Ribosomal protein S26e / Ribosomal protein S8e / Ribosomal protein S14 / Ribosomal protein S17e / Ribosomal protein S19e / Ribosomal protein S6e / Ribosomal protein S9 / Ribosomal protein S3Ae / Ribosomal protein S10 / Ribosomal protein S2 / Ribosomal protein S13 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S21e / Ribosomal protein S11 / Ribosomal protein S5 / Ribosomal protein S8 / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S27 / Ribosomal protein L41 / Ribosomal protein S27a / Ubiquitin family
40S ribosomal protein S24 / Ribosomal protein RPS15A / Ribosomal protein RPS28 / 40S ribosomal protein S29, putative / 40S ribosomal protein S3, putative / 40S ribosomal protein S25 / Ribosomal protein RPS27 / Ribosomal protein RPS19 / 40S ribosomal protein S9, putative / 40S ribosomal protein SA ...40S ribosomal protein S24 / Ribosomal protein RPS15A / Ribosomal protein RPS28 / 40S ribosomal protein S29, putative / 40S ribosomal protein S3, putative / 40S ribosomal protein S25 / Ribosomal protein RPS27 / Ribosomal protein RPS19 / 40S ribosomal protein S9, putative / 40S ribosomal protein SA / 40S ribosomal protein S4 / Uncharacterized protein / 40S ribosomal protein S12 / 40S ribosomal protein S2, putative / 40s ribosomal protein s17, putative / Ribosomal protein RPS10 / 40S ribosomal protein S6 / 40S ribosomal protein S30 / 40S ribosomal protein S15, putative / Ribosomal-ubiquitin protein RPS27A / 40S ribosomal protein S21 / 40S ribosomal protein S5, putative / 40S ribosomal protein S26 / 40S ribosomal protein S7 / 40S ribosomal protein S11, putative / 40S ribosomal protein S18, putative / Ribosomal protein RPS23 / 40S ribosomal protein S3a / 40s ribosomal protein S20, putative / 40S ribosomal protein S8 / Ribosomal protein RPS16 / 40S ribosomal protein S13, putative / 40s ribosomal protein S14, putative
Biological speciesToxoplasma gondii (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.35 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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJul 5, 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 24, 2018Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_refine_id

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Structure visualization

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Assembly

Deposited unit
2: 18S RNA
A: Ribosomal protein uS2
B: Ribosomal protein eS1
C: Ribosomal protein uS5
D: Ribosomal protein uS3
E: Ribosomal protein eS4
F: Ribosomal protein uS7
G: Ribosomal protein eS6
H: Ribosomal protein eS7
I: Ribosomal protein eS8
J: Ribosomal protein uS4
K: Ribosomal protein eS10
L: Ribosomal protein uS17
M: Ribosomal protein eS12
N: Ribosomal protein uS15
O: Ribosomal protein uS11
P: Ribosomal protein uS19
Q: Ribosomal protein uS9
R: Ribosomal protein eS17
S: Ribosomal protein uS13
T: Ribosomal protein eS19
U: Ribosomal protein uS10
V: Ribosomal protein eS21
W: Ribosomal protein uS8
X: Ribosomal protein uS12
Y: Ribosomal protein eS24
Z: Ribosomal protein eS25
a: Ribosomal protein eS26
b: Ribosomal protein eS27
c: Ribosomal protein eS28
d: Ribosomal protein uS14
e: Ribosomal protein eS30
f: Ribosomal protein eS31
m: Ribosomal protein eL41


Theoretical massNumber of molelcules
Total (without water)1,177,11334
Polymers1,177,11334
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area181100 Å2
ΔGint-1347 kcal/mol
Surface area381840 Å2

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Components

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RNA chain , 1 types, 1 molecules 2

#1: RNA chain 18S RNA


Mass: 576630.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote)

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Ribosomal protein ... , 33 types, 33 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZabcd...

#2: Protein Ribosomal protein uS2 /


Mass: 31546.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: Q8MPF7*PLUS
#3: Protein Ribosomal protein eS1 /


Mass: 29425.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: B9PGG2*PLUS
#4: Protein Ribosomal protein uS5 /


Mass: 29385.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: B9PZF2*PLUS
#5: Protein Ribosomal protein uS3 /


Mass: 26117.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A0F7UXI8*PLUS
#6: Protein Ribosomal protein eS4 /


Mass: 30204.713 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: Q1JSZ0*PLUS
#7: Protein Ribosomal protein uS7 /


Mass: 21650.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: B9PPE8*PLUS
#8: Protein Ribosomal protein eS6 /


Mass: 29027.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: B9PVR5*PLUS
#9: Protein Ribosomal protein eS7 /


Mass: 22631.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: B9PNL1*PLUS
#10: Protein Ribosomal protein eS8 /


Mass: 23615.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: B6KGK3*PLUS
#11: Protein Ribosomal protein uS4 /


Mass: 21731.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: B9PQU8*PLUS
#12: Protein Ribosomal protein eS10 /


Mass: 17428.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: B9PX63*PLUS
#13: Protein Ribosomal protein uS17 /


Mass: 18715.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: B9PMU7*PLUS
#14: Protein Ribosomal protein eS12 /


Mass: 15419.675 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: B9Q056*PLUS
#15: Protein Ribosomal protein uS15 /


Mass: 17211.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A125YSG6*PLUS
#16: Protein Ribosomal protein uS11 /


Mass: 16330.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A125YXW4*PLUS
#17: Protein Ribosomal protein uS19 /


Mass: 17190.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: B9PSN8*PLUS
#18: Protein Ribosomal protein uS9 /


Mass: 16587.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: B6KC70*PLUS
#19: Protein Ribosomal protein eS17 /


Mass: 15256.675 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: B9PXH2*PLUS
#20: Protein Ribosomal protein uS13 /


Mass: 17761.662 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: B9PMB3*PLUS
#21: Protein Ribosomal protein eS19 /


Mass: 18414.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A125YMR9*PLUS
#22: Protein Ribosomal protein uS10 /


Mass: 25943.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: B6KQG9*PLUS
#23: Protein Ribosomal protein eS21 /


Mass: 9049.265 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A125YS47*PLUS
#24: Protein Ribosomal protein uS8 /


Mass: 14973.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A125YJX3*PLUS
#25: Protein Ribosomal protein uS12 /


Mass: 15837.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: B9PHL8*PLUS
#26: Protein Ribosomal protein eS24 /


Mass: 15230.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A125YKH1*PLUS
#27: Protein Ribosomal protein eS25 /


Mass: 18707.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: S7V273*PLUS
#28: Protein Ribosomal protein eS26 /


Mass: 12753.630 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: B9PP49*PLUS
#29: Protein Ribosomal protein eS27 /


Mass: 9105.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A125YVX8*PLUS
#30: Protein Ribosomal protein eS28 /


Mass: 7601.858 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A125YJ29*PLUS
#31: Protein Ribosomal protein uS14 /


Mass: 6533.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: A0A0F7UYM7*PLUS
#32: Protein Ribosomal protein eS30 /


Mass: 6619.800 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: B9PTA0*PLUS
#33: Protein Ribosomal protein eS31 /


Mass: 17353.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: B9PQ37*PLUS
#34: Protein/peptide Ribosomal protein eL41 /


Mass: 5120.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Toxoplasma gondii (eukaryote) / References: UniProt: F0JB24*PLUS

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Details

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: Small subunit of Toxoplasma gondii ribosome / Type: RIBOSOME
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34
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

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
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: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 108162 / Symmetry type: POINT
RefinementHighest resolution: 3.35 Å

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