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

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Entry
Database: PDB / ID: 5xxb
TitleLarge subunit of Toxoplasma gondii ribosome
DescriptoruL2, uL3, uL4, uL18, eL6, uL30, eL8, uL6, uL16, uL5, eL13, eL14, eL15, uL13, uL22, eL18, eL19, eL20, eL21, eL22, uL14, eL24, uL23, uL24, eL27, uL15, eL29, eL30, eL31, eL32, eL33, eL34, uL29, eL36, eL37, eL38, eL39, eL40, eL42, eL43, eL28/RNA Complex
KeywordsRIBOSOME / parasitic ribosome / rRNA / rproteins
Specimen sourceToxoplasma gondii / eukaryote / トキソプラズマ, トクソプラズマ・ゴンディイ /
MethodElectron microscopy (3.17 Å resolution / Particle / Single particle)
AuthorsLi, Z. / Guo, Q. / Zheng, L. / Ji, Y. / Xie, Y. / Lai, D. / Lun, Z. / Suo, X. / Gao, N.
CitationCell Res., 2017

Cell Res., 2017 StrPapers
Cryo-EM structures of the 80S ribosomes from human parasites Trichomonas vaginalis and Toxoplasma gondii.
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 3, 2017 / Release: Aug 30, 2017

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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
Polyers2,027,34644
Non-polymers00
Water0
#1


  • idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)361790
ΔGint (kcal/M)-3074
Surface area (Å2)621290

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Components

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RNA chain , 3 types, 3 molecules 134

#1: RNA chain25S RNA


Mass: 1120153.125 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#2: RNA chain5S RNA


Mass: 39921.641 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#3: RNA chain5.8S RNA


Mass: 50787.980 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii

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Ribosomal protein ... , 41 types, 41 molecules ABCDEFGHIJ...

#4: Polypeptide(L)Ribosomal protein uL2


Mass: 28314.898 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#5: Polypeptide(L)Ribosomal protein uL3


Mass: 44150.738 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#6: Polypeptide(L)Ribosomal protein uL4


Mass: 45837.258 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#7: Polypeptide(L)Ribosomal protein uL18


Mass: 35408.742 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#8: Polypeptide(L)Ribosomal protein eL6


Mass: 21563.535 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#9: Polypeptide(L)Ribosomal protein uL30


Mass: 30187.777 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#10: Polypeptide(L)Ribosomal protein eL8


Mass: 31095.934 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#11: Polypeptide(L)Ribosomal protein uL6


Mass: 21459.178 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#12: Polypeptide(L)Ribosomal protein uL16


Mass: 24846.014 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#13: Polypeptide(L)Ribosomal protein uL5


Mass: 20240.361 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#14: Polypeptide(L)Ribosomal protein eL13


Mass: 39757.371 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#15: Polypeptide(L)Ribosomal protein eL14


Mass: 15492.432 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#16: Polypeptide(L)Ribosomal protein eL15


Mass: 24387.846 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#17: Polypeptide(L)Ribosomal protein uL13


Mass: 31757.688 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#18: Polypeptide(L)Ribosomal protein uL22


Mass: 22319.188 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#19: Polypeptide(L)Ribosomal protein eL18


Mass: 21223.158 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#20: Polypeptide(L)Ribosomal protein eL19


Mass: 22221.574 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#21: Polypeptide(L)Ribosomal protein eL20


Mass: 21372.252 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#22: Polypeptide(L)Ribosomal protein eL21


Mass: 17932.977 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#23: Polypeptide(L)Ribosomal protein eL22


Mass: 15103.659 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#24: Polypeptide(L)Ribosomal protein uL14


Mass: 14842.553 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#25: Polypeptide(L)Ribosomal protein eL24


Mass: 17644.857 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#26: Polypeptide(L)Ribosomal protein uL23


Mass: 18600.809 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#27: Polypeptide(L)Ribosomal protein uL24


Mass: 16353.228 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#28: Polypeptide(L)Ribosomal protein eL27


Mass: 16841.355 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#29: Polypeptide(L)Ribosomal protein uL15


Mass: 16384.355 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#30: Polypeptide(L)Ribosomal protein eL29


Mass: 6387.679 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#31: Polypeptide(L)Ribosomal protein eL30


Mass: 11682.658 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#32: Polypeptide(L)Ribosomal protein eL31


Mass: 14389.729 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#33: Polypeptide(L)Ribosomal protein eL32


Mass: 15652.334 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#34: Polypeptide(L)Ribosomal protein eL33


Mass: 12873.091 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#35: Polypeptide(L)Ribosomal protein eL34


Mass: 15427.309 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#36: Polypeptide(L)Ribosomal protein uL29


Mass: 14231.108 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#37: Polypeptide(L)Ribosomal protein eL36


Mass: 11437.687 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#38: Polypeptide(L)Ribosomal protein eL37


Mass: 11256.210 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#39: Polypeptide(L)Ribosomal protein eL38


Mass: 9606.386 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#40: Polypeptide(L)Ribosomal protein eL39


Mass: 6172.519 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#41: Polypeptide(L)Ribosomal protein eL40


Mass: 14714.291 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#42: Polypeptide(L)Ribosomal protein eL42


Mass: 12098.689 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#43: Polypeptide(L)Ribosomal protein eL43


Mass: 10426.384 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii
#44: Polypeptide(L)Ribosomal protein eL28


Mass: 14787.717 Da / Num. of mol.: 1 / Source: (natural) Toxoplasma gondii

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Details

Sequence detailsSequences 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

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Sample preparation

ComponentName: Large 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44
Source: NATURAL
Source (natural)Organism: Toxoplasma gondii
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

MicroscopyMicroscope model: 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 / Number of particles: 108162 / Symmetry type: POINT

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