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- PDB-3j79: Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound... -

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Entry
Database: PDB / ID: 3j79
TitleCryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine, large subunit
DescriptorPROTEIN/RNA Complex
KeywordsRIBOSOME/INHIBITOR / emetine / RIBOSOME-INHIBITOR complex
Specimen sourcePlasmodium falciparum / eukaryote / マラリア病原虫, 熱帯熱マラリア原虫, 熱帯熱病原虫 /
MethodElectron microscopy (3.2 Å resolution / Particle / Single particle)
AuthorsWong, W. / Bai, X.C. / Brown, A. / Fernandez, I.S. / Hanssen, E. / Condron, M. / Tan, Y.H. / Baum, J. / Scheres, S.H.W.
CitationElife, 2014, 3

Elife, 2014, 3 StrPapers
Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine.
Wilson Wong / Xiao-chen Bai / Alan Brown / Israel S Fernandez / Eric Hanssen / Melanie Condron / Yan Hong Tan / Jake Baum / Sjors H W Scheres

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 2, 2014 / Release: Jul 16, 2014
RevisionDateData content typeGroupProviderType
1.0Jul 16, 2014Structure modelrepositoryInitial release
1.1Dec 10, 2014Structure modelOther
1.2Dec 17, 2014Structure modelOther
1.3Jun 3, 2015Structure modelDatabase references

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Structure visualization

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Assembly

Deposited unit
A: 28S ribosomal RNA
B: 5S ribosomal RNA
C: 5.8S ribosomal RNA
D: 60S ribosomal protein uL2
E: 60S ribosomal protein uL3
F: 60S ribosomal protein uL4
G: 60S ribosomal protein uL5
H: 60S ribosomal protein uL6
I: 60S ribosomal protein eL6
J: 60S ribosomal protein eL8
K: 60S ribosomal protein uL13
L: 60S ribosomal protein eL13
M: 60S ribosomal protein uL14
N: 60S ribosomal protein eL14
O: 60S ribosomal protein uL15
P: 60S ribosomal protein eL15
Q: 60S ribosomal protein uL16
R: 60S ribosomal protein uL18
S: 60S ribosomal protein eL18
T: 60S ribosomal protein eL19
U: 60S ribosomal protein eL20
V: 60S ribosomal protein eL21
W: 60S ribosomal protein uL22
X: 60S ribosomal protein eL22
Y: 60S ribosomal protein uL23
Z: 60S ribosomal protein uL24
0: 60S ribosomal protein eL24
1: 60S ribosomal protein eL27
2: 60S ribosomal protein eL28
3: 60S ribosomal protein uL29
4: 60S ribosomal protein eL29
5: 60S ribosomal protein uL30
6: 60S ribosomal protein eL30
7: 60S ribosomal protein eL31
8: 60S ribosomal protein eL32
9: 60S ribosomal protein eL33
a: 60S ribosomal protein eL34
b: 60S ribosomal protein eL36
c: 60S ribosomal protein eL37
d: 60S ribosomal protein eL38
e: 60S ribosomal protein eL39
f: 60S ribosomal protein eL40
g: 60S ribosomal protein eL41
h: 60S ribosomal protein eL43
i: 60S ribosomal protein eL44
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,135,889213
Polyers2,131,60045
Non-polymers4,289168
Water0
#1


  • idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 3 types, 3 molecules ABC

#1: RNA chain28S ribosomal RNA


Mass: 1216212.125 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum
#2: RNA chain5S ribosomal RNA


Mass: 38410.859 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum
#3: RNA chain5.8S ribosomal RNA


Mass: 51206.461 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum

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60S ribosomal protein ... , 42 types, 42 molecules DEFGHIJKLM...

#4: Polypeptide(L)60S ribosomal protein uL2


Mass: 28064.998 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8I3T9

Cellular component

Molecular function

Biological process

#5: Polypeptide(L)60S ribosomal protein uL3


Mass: 44318.180 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8IJC6

Cellular component

Molecular function

Biological process

#6: Polypeptide(L)60S ribosomal protein uL4


Mass: 46311.688 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8I431

Cellular component

Molecular function

Biological process

#7: Polypeptide(L)60S ribosomal protein uL5


Mass: 20268.666 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8IBQ6

Cellular component

Molecular function

Biological process

#8: Polypeptide(L)60S ribosomal protein uL6


Mass: 21638.562 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8IE85

Cellular component

Molecular function

Biological process

#9: Polypeptide(L)60S ribosomal protein eL6


Mass: 25587.623 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8IDV1

Cellular component

Molecular function

Biological process

#10: Polypeptide(L)60S ribosomal protein eL8


Mass: 32760.455 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8ILL2

Cellular component

Molecular function

Biological process

#11: Polypeptide(L)60S ribosomal protein uL13


Mass: 23805.344 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8IJZ7

Cellular component

Molecular function

Biological process

#12: Polypeptide(L)60S ribosomal protein eL13


Mass: 25508.193 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8IAX6

Cellular component

Molecular function

Biological process

#13: Polypeptide(L)60S ribosomal protein uL14


Mass: 15015.713 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8IE09

Cellular component

Molecular function

Biological process

#14: Polypeptide(L)60S ribosomal protein eL14


Mass: 19340.373 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8ILE8

Cellular component

Molecular function

Biological process

#15: Polypeptide(L)60S ribosomal protein uL15


Mass: 16765.834 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: C6KT23

Cellular component

Molecular function

Biological process

#16: Polypeptide(L)60S ribosomal protein eL15


Mass: 24197.660 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: C0H4A6

Cellular component

Molecular function

Biological process

#17: Polypeptide(L)60S ribosomal protein uL16


Mass: 25265.480 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8ILV2

Cellular component

Molecular function

Biological process

#18: Polypeptide(L)60S ribosomal protein uL18


Mass: 34067.352 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8ILL3

Cellular component

Molecular function

Biological process

#19: Polypeptide(L)60S ribosomal protein eL18


Mass: 21508.783 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: C0H5G3

Cellular component

Molecular function

Biological process

#20: Polypeptide(L)60S ribosomal protein eL19


Mass: 21641.096 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: C6KSY6

Cellular component

Molecular function

Biological process

#21: Polypeptide(L)60S ribosomal protein eL20


Mass: 21793.611 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8IDS6

Cellular component

Molecular function

Biological process

#22: Polypeptide(L)60S ribosomal protein eL21


Mass: 18840.244 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8ILK3

Cellular component

Molecular function

Biological process

#23: Polypeptide(L)60S ribosomal protein uL22


Mass: 23469.926 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8IDI5

Cellular component

Molecular function

Biological process

#24: Polypeptide(L)60S ribosomal protein eL22


Mass: 16422.930 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8IB51

Cellular component

Molecular function

Biological process

#25: Polypeptide(L)60S ribosomal protein uL23


Mass: 22152.748 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8IE82

Cellular component

Molecular function

Biological process

#26: Polypeptide(L)60S ribosomal protein uL24


Mass: 14855.709 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: O77364

Cellular component

Molecular function

Biological process

#27: Polypeptide(L)60S ribosomal protein eL24


Mass: 19295.930 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8IEM3

Cellular component

Molecular function

Biological process

#28: Polypeptide(L)60S ribosomal protein eL27


Mass: 16785.180 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8IKM5

Cellular component

Molecular function

Biological process

#29: Polypeptide(L)60S ribosomal protein eL28


Mass: 14437.823 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8IHU0

Cellular component

Molecular function

Biological process

#30: Polypeptide(L)60S ribosomal protein uL29


Mass: 14787.824 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8IIB4

Cellular component

Molecular function

Biological process

  • maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000463)
  • translation (GO: 0006412)
#31: Polypeptide(L)60S ribosomal protein eL29


Mass: 8041.588 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: C6S3J6

Cellular component

Molecular function

Biological process

#32: Polypeptide(L)60S ribosomal protein uL30


Mass: 30593.184 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: O97250

Cellular component

Molecular function

Biological process

#33: Polypeptide(L)60S ribosomal protein eL30


Mass: 11794.760 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8IJK8

Cellular component

Molecular function

Biological process

#34: Polypeptide(L)60S ribosomal protein eL31


Mass: 14099.854 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8I463

Cellular component

Molecular function

Biological process

#35: Polypeptide(L)60S ribosomal protein eL32


Mass: 15565.751 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8I3B0

Cellular component

Molecular function

Biological process

#36: Polypeptide(L)60S ribosomal protein eL33


Mass: 16306.425 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8IHT9

Cellular component

Molecular function

Biological process

#37: Polypeptide(L)60S ribosomal protein eL34


Mass: 17406.967 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8IBY4

Cellular component

Molecular function

Biological process

#38: Polypeptide(L)60S ribosomal protein eL36


Mass: 12825.440 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8I713

Cellular component

Molecular function

Biological process

#39: Polypeptide(L)60S ribosomal protein eL37


Mass: 10571.592 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: C0H4L5

Cellular component

Molecular function

Biological process

#40: Polypeptide(L)60S ribosomal protein eL38


Mass: 10341.729 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8II62

Cellular component

Molecular function

Biological process

#41: Polypeptide(L)60S ribosomal protein eL39


Mass: 6540.912 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: C0H4H3

Cellular component

Molecular function

Biological process

#42: Polypeptide(L)60S ribosomal protein eL40


Mass: 14645.169 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8ID50

Cellular component

Molecular function

Biological process

#43: Polypeptide(L)60S ribosomal protein eL41


Mass: 5108.310 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: C6S3G4

Cellular component

Molecular function

Biological process

#44: Polypeptide(L)60S ribosomal protein eL43


Mass: 10826.083 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: O96184

Cellular component

Molecular function

Biological process

#45: Polypeptide(L)60S ribosomal protein eL44


Mass: 12194.902 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: O97231

Cellular component

Molecular function

Biological process

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Non-polymers , 2 types, 168 molecules

#46: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 163 / Formula: Mg
#47: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Formula: Zn

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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: Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine
Type: RIBOSOME
Molecular weightValue: 4.2 deg. / Units: MEGADALTONS / Experimental value: NO
Buffer solutionName: 20 mM HEPES, pH 7.4, 40 mM potassium acetate, 10 mM ammonium acetate, 10 mM magnesium acetate, 5 mM BME
Details: 20 mM HEPES, pH 7.4, 40 mM potassium acetate, 10 mM ammonium acetate, 10 mM magnesium acetate, 5 mM BME
pH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: holey carbon grids (Quantifoil R2/2) with home-made continuous carbon film, glow-discharged 30 seconds
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temp: 90 K / Humidity: 100 %
Details: Blot 2.5 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Method: Blot 2.5 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300 / Date: Jan 19, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 78000 / Calibrated magnification: 104748 / Nominal defocus max: 3800 nm / Nominal defocus min: 800 nm / Cs: 2 mm
Specimen holderSpecimen holder type: GATAN LIQUID NITROGEN / Temperature: 85 kelvins / Temperature (max): 90 kelvins / Temperature (min): 80 kelvins
Image recordingElectron dose: 20 e/Å2
Details: An in-house system was used to intercept videos from the detector at a rate of 17 frames/second (1 second exposures).
Film or detector model: FEI FALCON II (4k x 4k)
Image scansNumber digital images: 1083
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: REFMAC / Version: 5.8.0077 2014/05/16 / Classification: refinement / Contact author: Garib N. Murshudov / Contact author email: garib@mrc-lmb.cam.ac.uk
Description: (un)restrained refinement or idealisation of macromolecular structures
EM software
IDNameVersionCategory
1CTFFIND3CTF CORRECTION
2RelionRECONSTRUCTION
CTF correctionDetails: Each particle
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 105247 / Nominal pixel size: 1.34 / Actual pixel size: 1.34
Details: A newly developed statistical movie processing approach was used to compensate for beam-induced movement.
Refinement type: HALF-MAPS REFINED INDEPENDENTLY / Symmetry type: POINT
Number of atoms included #LASTProtein: 50662 / Nucleic acid: 73684 / Ligand: 168 / Solvent: 0 / Total: 124514

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