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- PDB-5xy3: Large subunit of Trichomonas vaginalis ribosome -

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Entry
Database: PDB / ID: 5xy3
TitleLarge subunit of Trichomonas vaginalis ribosome
DescriptorUncharacterized protein
Ribosomal protein
Ubiquitin
putative/RNA Complex
(Ribosomal protein ...) x 23
(60S ribosomal protein ...) x 11
KeywordsRIBOSOME / Trichomonas vaginalis ribosome / rRNA / rprotein
Specimen sourceTrichomonas vaginalis / eukaryote / ちつほねまくむし, 膣トリコモナス
MethodElectron microscopy (3.2 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 6, 2017 / Release: Aug 30, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 30, 2017Structure modelrepositoryInitial release
1.1Sep 6, 2017Structure modelStructure summaryentity_entity.pdbx_description

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Assembly

Deposited unit
1: 25S ribosomal RNA
3: 5S ribosomal RNA
4: 5.8S ribosomal RNA
A: Ribosomal protein L8, putative
B: Uncharacterized protein
C: Ribosomal protein, putative
D: Ribosomal protein L5
E: 60S ribosomal protein L6, putative
F: Ribosomal protein L30p/L7e, putative
G: Ribosomal protein L7Ae, putative
H: Ribosomal protein L6, putative
I: Ribosomal protein, putative
J: 60S ribosomal protein L11, putative
L: Ribosomal protein L13e, putative
M: Ribosomal protein L14, putative
N: Ribosomal protein L15
O: Ribosomal protein L13, putative
P: Ribosomal protein L22, putative
Q: 60S ribosomal protein L18, putative
R: 60S ribosomal protein L19-3, putative
S: 60S ribosomal protein L18a
T: Ribosomal protein L21e, putative
U: 60S ribosomal protein L22-1, putative
V: 60S ribosomal protein L23, putative
W: Ribosomal protein L24e, putative
X: Ribosomal protein L23, putative
Y: Ribosomal protein L24, putative
Z: Ribosomal protein L27e, putative
a: Uncharacterized protein
b: 60S ribosomal protein L29
c: 60S ribosomal protein L30, putative
d: Ribosomal protein L31e, putative
e: Ribosomal protein L32, putative
f: Ribosomal protein L35Ae, putative
g: Ribosomal protein L34e, putative
h: Ribosomal protein L29, putative
i: Ribosomal protein L36e, putative
j: Ribosomal protein L37
k: Ribosomal protein L38e, putative
l: 60S ribosomal protein L39, putative
m: Ubiquitin, putative
o: 60S ribosomal protein L44, putative
p: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)1,713,54043
Polyers1,713,54043
Non-polymers00
Water0
#1


  • idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)308510
ΔGint (kcal/M)-2751
Surface area (Å2)556640

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Components

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RNA chain , 3 types, 3 molecules 134

#1: RNA chain25S ribosomal RNA


Mass: 892223.312 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: GenBank: 7243609
#2: RNA chain5S ribosomal RNA


Mass: 37963.594 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: GenBank: 68235680
#3: RNA chain5.8S ribosomal RNA


Mass: 52173.945 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: GenBank: 461415

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Ribosomal protein ... , 23 types, 23 molecules ADFGHLMNOP...

#4: Polypeptide(L)Ribosomal protein L8, putative / uL2


Mass: 26949.082 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2E6Z8
#7: Polypeptide(L)Ribosomal protein L5 / uL18


Mass: 34932.766 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2DNM5
#9: Polypeptide(L)Ribosomal protein L30p/L7e, putative / uL30


Mass: 26842.281 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2F592
#10: Polypeptide(L)Ribosomal protein L7Ae, putative / eL8


Mass: 27602.273 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2ET60
#11: Polypeptide(L)Ribosomal protein L6, putative / uL6


Mass: 22930.506 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2DDT1
#14: Polypeptide(L)Ribosomal protein L13e, putative / eL13


Mass: 21865.705 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2G4E1
#15: Polypeptide(L)Ribosomal protein L14, putative / eL14


Mass: 14726.112 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2DZ49
#16: Polypeptide(L)Ribosomal protein L15 / eL15


Mass: 24323.465 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2ECR7
#17: Polypeptide(L)Ribosomal protein L13, putative / uL13


Mass: 22569.111 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2DZ26
#18: Polypeptide(L)Ribosomal protein L22, putative / uL22


Mass: 18530.490 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2DM53
#22: Polypeptide(L)Ribosomal protein L21e, putative / eL21


Mass: 17910.867 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2F2S5
#25: Polypeptide(L)Ribosomal protein L24e, putative / eL24


Mass: 13282.475 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2DJQ1
#26: Polypeptide(L)Ribosomal protein L23, putative / uL23


Mass: 15582.249 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2DUV8
#27: Polypeptide(L)Ribosomal protein L24, putative / uL24


Mass: 15782.617 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2DKF2
#28: Polypeptide(L)Ribosomal protein L27e, putative / eL27


Mass: 15946.061 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2DNC1
#32: Polypeptide(L)Ribosomal protein L31e, putative / eL31


Mass: 12446.528 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2D9N8
#33: Polypeptide(L)Ribosomal protein L32, putative / eL32


Mass: 15249.669 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2F2J0
#34: Polypeptide(L)Ribosomal protein L35Ae, putative / eL33


Mass: 11668.678 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2DSF3
#35: Polypeptide(L)Ribosomal protein L34e, putative / eL34


Mass: 13346.646 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2FWA1
#36: Polypeptide(L)Ribosomal protein L29, putative / uL29


Mass: 14300.049 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2E6R2
#37: Polypeptide(L)Ribosomal protein L36e, putative / eL36


Mass: 10941.717 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2EXW7
#38: Polypeptide(L)Ribosomal protein L37 / eL37


Mass: 9355.945 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2F8Y8
#39: Polypeptide(L)Ribosomal protein L38e, putative / eL38


Mass: 8468.960 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2FFH9

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Uncharacterized ... , 3 types, 3 molecules Bap

#5: Polypeptide(L)Uncharacterized protein / uL3


Mass: 46904.270 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2DD62
#29: Polypeptide(L)Uncharacterized protein / uL15


Mass: 17006.787 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2DHU7
#43: Polypeptide(L)Uncharacterized protein / eL43


Mass: 10051.994 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2DEM7

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Ribosomal protein, ... , 2 types, 2 molecules CI

#6: Polypeptide(L)Ribosomal protein, putative / uL4


Mass: 40320.738 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2E4D0
#12: Polypeptide(L)Ribosomal protein, putative / uL16


Mass: 23800.781 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2FVZ6

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60S ribosomal protein ... , 11 types, 11 molecules EJQRSUVbclo

#8: Polypeptide(L)60S ribosomal protein L6, putative / eL6


Mass: 16045.772 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2FXW1
#13: Polypeptide(L)60S ribosomal protein L11, putative / uL5


Mass: 19373.488 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2E7L8
#19: Polypeptide(L)60S ribosomal protein L18, putative / eL18


Mass: 21122.545 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2D7Q5
#20: Polypeptide(L)60S ribosomal protein L19-3, putative / eL19


Mass: 21056.785 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2D8G1
#21: Polypeptide(L)60S ribosomal protein L18a / eL20


Mass: 19853.973 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2EP03
#23: Polypeptide(L)60S ribosomal protein L22-1, putative / eL22


Mass: 12237.054 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2DNV5
#24: Polypeptide(L)60S ribosomal protein L23, putative / uL14


Mass: 14840.554 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2DP51
#30: Polypeptide(L)60S ribosomal protein L29 / eL29


Mass: 6823.724 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2DM33
#31: Polypeptide(L)60S ribosomal protein L30, putative / eL30


Mass: 12316.229 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2E6Z9
#40: Polypeptide(L)60S ribosomal protein L39, putative / eL39


Mass: 6297.775 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2D9N4
#42: Polypeptide(L)60S ribosomal protein L44, putative / eL41


Mass: 12471.015 Da / Num. of mol.: 1 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2DAI6

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Polypeptide(L) , 1 types, 1 molecules m

#41: Polypeptide(L)Ubiquitin, putative / eL40


Mass: 15101.515 Da / Num. of mol.: 1 / Fragment: UNP residues 35-166 / Source: (natural) Trichomonas vaginalis / References: UniProt: A2DGL5

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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 Trichomonas vaginalis 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
Source: NATURAL
Source (natural)Organism: Trichomonas vaginalis
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 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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 57162 / Symmetry type: POINT

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