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Entry
Database: PDB / ID: 3j7a
TitleCryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine, small 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 Yorodumi Papers
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 3, 2014 / Release: Jul 16, 2014
RevisionDateData content typeGroupProviderType
1.0Jul 16, 2014Structure modelrepositoryInitial release
1.1Apr 8, 2015Structure modelStructure summary
1.2Jun 3, 2015Structure modelDatabase references

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Assembly

Deposited unit
A: 18S ribosomal RNA
B: 40S ribosomal protein eS1
C: 40S ribosomal protein uS2
D: 40S ribosomal protein uS3
E: 40S ribosomal protein uS4
F: 40S ribosomal protein eS4
G: 40S ribosomal protein uS5
H: 40S ribosomal protein eS6
I: 40S ribosomal protein uS7
J: 40S ribosomal protein eS7
K: 40S ribosomal protein uS8
L: 40S ribosomal protein eS8
M: 40S ribosomal protein uS9
N: 40S ribosomal protein uS10
O: 40S ribosomal protein eS10
P: 40S ribosomal protein uS11
Q: 40S ribosomal protein uS12
R: 40S ribosomal protein eS12
S: 40S ribosomal protein uS13
T: 40S ribosomal protein uS14
U: 40S ribosomal protein uS15
V: 40S ribosomal protein uS17
W: 40S ribosomal protein eS17
X: 40S ribosomal protein uS19
Y: 40S ribosomal protein eS19
Z: 40S ribosomal protein eS21
1: 40S ribosomal protein eS24
2: 40S ribosomal protein eS25
3: 40S ribosomal protein eS26
4: 40S ribosomal protein eS27
5: 40S ribosomal protein eS28
6: 40S ribosomal protein eS30
7: tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,263,060102
Polyers1,260,88533
Non-polymers2,17469
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 2 types, 2 molecules A7

#1: RNA chain18S ribosomal RNA


Mass: 671337.500 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum
#33: RNA chaintRNA


Mass: 23774.059 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum

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40S ribosomal protein ... , 31 types, 31 molecules BCDEFGHIJK...

#2: Polypeptide(L)40S ribosomal protein eS1


Mass: 30111.678 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: O97313

Cellular component

Molecular function

Biological process

#3: Polypeptide(L)40S ribosomal protein uS2


Mass: 29891.182 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8IJD4

Cellular component

Molecular function

Biological process

  • endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000447)
  • endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000461)
  • ribosomal small subunit assembly (GO: 0000028)
  • rRNA export from nucleus (GO: 0006407)
  • translation (GO: 0006412)
#4: Polypeptide(L)40S ribosomal protein uS3


Mass: 24709.908 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8IKH8

Cellular component

Molecular function

Biological process

#5: Polypeptide(L)40S ribosomal protein uS4


Mass: 22172.076 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8I3R0

Cellular component

Molecular function

Biological process

#6: Polypeptide(L)40S ribosomal protein eS4


Mass: 29830.330 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8IIU8

Cellular component

Molecular function

Biological process

#7: Polypeptide(L)40S ribosomal protein uS5


Mass: 30008.768 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8IL02

Cellular component

Molecular function

Biological process

#8: Polypeptide(L)40S ribosomal protein eS6


Mass: 35473.766 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8IDR9

Cellular component

Molecular function

Biological process

#9: Polypeptide(L)40S ribosomal protein uS7


Mass: 21898.484 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8IBN5

Cellular component

Molecular function

Biological process

#10: Polypeptide(L)40S ribosomal protein eS7


Mass: 22524.740 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8IET7

Cellular component

Molecular function

Biological process

#11: Polypeptide(L)40S ribosomal protein uS8


Mass: 14900.678 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: O77395

Cellular component

Molecular function

Biological process

#12: Polypeptide(L)40S ribosomal protein eS8


Mass: 25105.992 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8IM10

Cellular component

Molecular function

Biological process

  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
  • translation (GO: 0006412)
#13: Polypeptide(L)40S ribosomal protein uS9


Mass: 16318.242 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8IAX5

Cellular component

Molecular function

Biological process

  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
  • translation (GO: 0006412)
#14: Polypeptide(L)40S ribosomal protein uS10


Mass: 13534.918 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8IK02

Cellular component

Molecular function

Biological process

#15: Polypeptide(L)40S ribosomal protein eS10


Mass: 16510.201 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8IBQ5

Cellular component

Molecular function

Biological process

#16: Polypeptide(L)40S ribosomal protein uS11


Mass: 16105.612 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8I3U6

Cellular component

Molecular function

Biological process

  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
  • ribosomal small subunit assembly (GO: 0000028)
  • translation (GO: 0006412)
#17: Polypeptide(L)40S ribosomal protein uS12


Mass: 16166.962 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: O97248

Cellular component

Molecular function

Biological process

#18: Polypeptide(L)40S ribosomal protein eS12


Mass: 15414.444 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: O97249

Cellular component

Molecular function

Biological process

#19: Polypeptide(L)40S ribosomal protein uS13


Mass: 17928.947 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8IIA2

Cellular component

Molecular function

Biological process

#20: Polypeptide(L)40S ribosomal protein uS14


Mass: 6430.679 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: C0H4K8

Cellular component

Molecular function

Biological process

#21: Polypeptide(L)40S ribosomal protein uS15


Mass: 17286.469 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8IDB0

Cellular component

Molecular function

Biological process

#22: Polypeptide(L)40S ribosomal protein uS17


Mass: 18801.189 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: O77381

Cellular component

Molecular function

Biological process

#23: Polypeptide(L)40S ribosomal protein eS17


Mass: 16096.985 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8I502

Cellular component

Molecular function

Biological process

#24: Polypeptide(L)40S ribosomal protein uS19


Mass: 16800.764 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: C0H5C2

Cellular component

Molecular function

Biological process

#25: Polypeptide(L)40S ribosomal protein eS19


Mass: 19757.920 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8IFP2

Cellular component

Molecular function

Biological process

#26: Polypeptide(L)40S ribosomal protein eS21


Mass: 9157.478 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8IHS5

Cellular component

Molecular function

Biological process

  • endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000447)
  • endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000461)
  • translation (GO: 0006412)
#27: Polypeptide(L)40S ribosomal protein eS24


Mass: 15431.478 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8I3R6

Cellular component

Molecular function

Biological process

  • maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO: 0000462)
  • translation (GO: 0006412)
#28: Polypeptide(L)40S ribosomal protein eS25


Mass: 11691.931 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8ILN8

Cellular component

Molecular function

Biological process

#29: Polypeptide(L)40S ribosomal protein eS26


Mass: 12539.681 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: O96258

Cellular component

Molecular function

Biological process

#30: Polypeptide(L)40S ribosomal protein eS27


Mass: 9154.856 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8IEN2

Cellular component

Molecular function

Biological process

#31: Polypeptide(L)40S ribosomal protein eS28


Mass: 7508.800 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: Q8IKL9

Cellular component

Molecular function

Biological process

#32: Polypeptide(L)40S ribosomal protein eS30


Mass: 6508.725 Da / Num. of mol.: 1 / Source: (natural) Plasmodium falciparum / References: UniProt: O96269

Cellular component

Molecular function

Biological process

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Non-polymers , 3 types, 69 molecules

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


Mass: 24.305 Da / Num. of mol.: 67 / Formula: Mg
#35: ChemicalChemComp-34G / emetine / (3beta,14beta)-6',7',10,11-tetramethoxyemetan


Mass: 480.639 Da / Num. of mol.: 1 / Formula: C29H40N2O4
#36: ChemicalChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / 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: 32915 / Nucleic acid: 35848 / Ligand: 103 / Solvent: 0 / Total: 68866

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