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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 / homologyRibosomal protein S11 superfamily / Ribosomal protein S5, N-terminal domain / Ribosomal protein S12/S23 / Ribosomal protein S7p/S5e / Ribosomal protein S3, C-terminal domain / Ribosomal protein S19 / Ubiquitin family / Ribosomal protein S14p/S29e / Ribosomal protein S15 / Ribosomal protein S2 ...Ribosomal protein S11 superfamily / Ribosomal protein S5, N-terminal domain / Ribosomal protein S12/S23 / Ribosomal protein S7p/S5e / Ribosomal protein S3, C-terminal domain / Ribosomal protein S19 / Ubiquitin family / Ribosomal protein S14p/S29e / Ribosomal protein S15 / Ribosomal protein S2 / Ribosomal protein S10p/S20e / S27a-like superfamily / Ribosomal protein S17 / Ribosomal protein S9/S16 / Ribosomal protein S8 / Ribosomal protein S11 / Ribosomal protein S13/S18 / KOW motif / Ribosomal S17 / Ribosomal family S4e / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S21e superfamily / Ribosomal protein S19e / Ribosomal protein S8 superfamily / Ribosomal protein S2, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S28e conserved site / 50S ribosomal protein L30e-like / Ubiquitin-like domain superfamily / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / Winged helix-like DNA-binding domain superfamily / Ribosomal protein S26e superfamily / Winged helix DNA-binding domain superfamily / Ribosomal protein S17e-like superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S10 domain superfamily / RNA-binding S4 domain superfamily / 40S Ribosomal protein S10 / Ribosomal protein S19e domain superfamily / Ribosomal protein S4e, central domain superfamily / Ribosomal S3Ae family / Ribosomal protein S6e / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13 signature. / Ribosomal protein S19 signature. / Ribosomal protein S9 signature. / Ribosomal protein S15 signature. / Ribosomal protein S14 signature. / Ribosomal protein S4e signature. / Ribosomal protein S24e signature. / Ribosomal protein S6e signature. / Ribosomal protein S4 signature. / Ribosomal protein S17e signature. / Ribosomal protein S12 signature. / Ribosomal protein S26e signature. / Ribosomal protein S28e signature. / Ribosomal protein S2 signature 1. / Ribosomal protein S2 signature 2. / Ribosomal protein S21e signature. / Ribosomal protein S12e signature. / Ubiquitin domain profile. / Ribosomal protein S13 family profile. / Ribosomal protein S17 signature. / Ribosomal protein S11 signature. / Ribosomal protein S28e / Ribosomal protein S27 / Ribosomal protein S8e / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein S21e / Ribosomal protein S7e / Ribosomal protein S24e / Ribosomal protein S26e / S4 domain / Ribosomal protein S27a / S25 ribosomal protein / Ribosomal protein S7 signature. / Plectin/S10 domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S30 / Ribosomal protein L41 / KH domain / Ribosomal S13/S15 N-terminal domain / RS4NT (NUC023) domain / 40S ribosomal protein S4 C-terminus / Ribosomal_S17 N-terminal / Ribosomal protein S10 domain / Ribosomal protein S7 domain / S5 double stranded RNA-binding domain profile. / Ribosomal protein S27a / Ribosomal protein S2 / Ribosomal protein S13 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S21e / Ribosomal protein S11 / Ribosomal protein S24e / Ribosomal protein S19/S15 / RNA-binding S4 domain
Function and homology information
Specimen sourceToxoplasma gondii (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.35 Å resolution
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 5, 2017 / Release: Aug 30, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 30, 2017Structure modelrepositoryInitial release
1.1Oct 18, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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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
Polyers1,177,11334
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)181100
ΔGint (kcal/M)-1347
Surface area (Å2)381840

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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: (natural) Toxoplasma gondii (eukaryote)

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

#2: Protein/peptide Ribosomal protein uS2 /


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


Mass: 5120.324 Da / Num. of mol.: 1 / 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 / 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
MicroscopyMicroscope model: 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 / Number of particles: 108162 / Symmetry type: POINT
Least-squares processHighest resolution: 3.35 Å

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