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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
Components
  • (60S ribosomal protein ...) x 42
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
KeywordsRIBOSOME/INHIBITOR / emetine / RIBOSOME-INHIBITOR complex
Function / homologyRibosomal protein L34Ae superfamily / Ribosomal protein L5 / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L27e superfamily / Ribosomal protein L35A superfamily / Ribosomal protein L30/YlxQ / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L22p/L17e / Ribosomal protein L14p/L23e / Ubiquitin family ...Ribosomal protein L34Ae superfamily / Ribosomal protein L5 / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L27e superfamily / Ribosomal protein L35A superfamily / Ribosomal protein L30/YlxQ / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L22p/L17e / Ribosomal protein L14p/L23e / Ubiquitin family / Ribosomal protein L16p/L10e / Ribosomal protein L23 / Ribosomal protein L3 / Ribosomal protein L22e superfamily / Ribosomal protein L30p/L7e / Ribosomal protein L6 / KOW motif / Ribosomal protein L13 / Ribosomal protein L4/L1 family / ribosomal L5P family C-terminus / Ribosomal L15 / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal L29 protein / Ribosomal L39 protein / Ribosomal protein L44 / Ribosomal protein L40e superfamily / Ribosomal protein L7A/L8 superfamily / Ribosomal protein L21e / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / 60S ribosomal protein L4, C-terminal domain / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L28e/Mak16 / 50S ribosomal protein L30e-like / Ubiquitin-like domain superfamily / Ribosomal protein L15 / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / Ribosomal protein L19, eukaryotic / Ribosomal protein L19/L19e superfamily / Ribosomal protein L38e superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L32e superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L21 superfamily / Ribosomal protein L36e domain superfamily / Ribosomal L40e family / Ribosomal protein L36e / Ribosomal protein L39e domain superfamily / Ribosomal protein L18e signature. / Ribosomal protein L39e signature. / Ubiquitin domain signature. / Ribosomal protein L2 signature. / Ribosomal protein L3 signature. / Ribosomal protein L15 signature. / Ribosomal protein L32e signature. / Ribosomal protein L30e signature 1. / Ribosomal protein L30e signature 2. / Ribosomal protein L37e signature. / Ribosomal protein L13e signature. / Ribosomal protein L31e signature. / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L34e signature. / Ribosomal protein L21e signature. / Ribosomal protein L44e signature. / Ribosomal protein L36e signature. / Ribosomal protein L15e signature. / Ribosomal protein L10e signature. / Ubiquitin domain profile. / Translesion Synthesis by POLH / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / MAPK6/MAPK4 signaling / Ribosomal protein L23 signature. / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L6e / Ribosomal L27e protein family / Ribosomal protein L31e / Ribosomal protein L34e / Ribosomal protein L24e / Ribosomal protein L35Ae / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein L19e / Ribosomal protein L13e / Ribosomal protein L32 / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal L22e protein family / Ribosomal L28e protein family / Ribosomal proteins L26 eukaryotic, L24P archaeal / Ribosomal L29e protein family / Ribosomal L37ae protein family / Ribosomal L38e protein family / Ribosomal protein L37e / Ribosomal protein L14
Function and homology information
Specimen sourcePlasmodium falciparum (malaria parasite P. falciparum)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.2 Å resolution
AuthorsWong, W. / Bai, X.C. / Brown, A. / Fernandez, I.S. / Hanssen, E. / Condron, M. / Tan, Y.H. / Baum, J. / Scheres, S.H.W.
CitationJournal: Elife / Year: 2014
Title: Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine.
Authors: 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 typeGroupCategoryItemProviderType
1.0Jul 16, 2014Structure modelrepositoryInitial release
1.1Dec 10, 2014Structure modelOther
1.2Dec 17, 2014Structure modelOther
1.3Jun 3, 2015Structure modelDatabase references
1.4Jul 18, 2018Structure modelData collectionem_software_em_software.image_processing_id / _em_software.name

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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 chain 28S ribosomal RNA /


Mass: 1216212.125 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7
#2: RNA chain 5S ribosomal RNA /


Mass: 38410.859 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7
#3: RNA chain 5.8S ribosomal RNA /


Mass: 51206.461 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7

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60S ribosomal protein ... , 42 types, 42 molecules DEFGHIJKLMNOPQRSTUVWXYZ0123456...

#4: Protein/peptide 60S ribosomal protein uL2 /


Mass: 28064.998 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8I3T9
#5: Protein/peptide 60S ribosomal protein uL3 /


Mass: 44318.180 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IJC6
#6: Protein/peptide 60S ribosomal protein uL4 /


Mass: 46311.688 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8I431
#7: Protein/peptide 60S ribosomal protein uL5 /


Mass: 20268.666 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IBQ6
#8: Protein/peptide 60S ribosomal protein uL6 /


Mass: 21638.562 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IE85
#9: Protein/peptide 60S ribosomal protein eL6 /


Mass: 25587.623 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IDV1
#10: Protein/peptide 60S ribosomal protein eL8 /


Mass: 32760.455 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8ILL2
#11: Protein/peptide 60S ribosomal protein uL13 /


Mass: 23805.344 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IJZ7
#12: Protein/peptide 60S ribosomal protein eL13 /


Mass: 25508.193 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IAX6
#13: Protein/peptide 60S ribosomal protein uL14 /


Mass: 15015.713 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IE09
#14: Protein/peptide 60S ribosomal protein eL14 /


Mass: 19340.373 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8ILE8
#15: Protein/peptide 60S ribosomal protein uL15 /


Mass: 16765.834 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: C6KT23
#16: Protein/peptide 60S ribosomal protein eL15 /


Mass: 24197.660 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: C0H4A6
#17: Protein/peptide 60S ribosomal protein uL16 /


Mass: 25265.480 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8ILV2
#18: Protein/peptide 60S ribosomal protein uL18 /


Mass: 34067.352 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8ILL3
#19: Protein/peptide 60S ribosomal protein eL18 /


Mass: 21508.783 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: C0H5G3
#20: Protein/peptide 60S ribosomal protein eL19 /


Mass: 21641.096 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: C6KSY6
#21: Protein/peptide 60S ribosomal protein eL20 /


Mass: 21793.611 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IDS6
#22: Protein/peptide 60S ribosomal protein eL21 /


Mass: 18840.244 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8ILK3
#23: Protein/peptide 60S ribosomal protein uL22 /


Mass: 23469.926 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IDI5
#24: Protein/peptide 60S ribosomal protein eL22 /


Mass: 16422.930 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IB51
#25: Protein/peptide 60S ribosomal protein uL23 /


Mass: 22152.748 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IE82
#26: Protein/peptide 60S ribosomal protein uL24 /


Mass: 14855.709 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: O77364
#27: Protein/peptide 60S ribosomal protein eL24 /


Mass: 19295.930 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IEM3
#28: Protein/peptide 60S ribosomal protein eL27 /


Mass: 16785.180 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IKM5
#29: Protein/peptide 60S ribosomal protein eL28 /


Mass: 14437.823 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IHU0
#30: Protein/peptide 60S ribosomal protein uL29 /


Mass: 14787.824 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IIB4
#31: Protein/peptide 60S ribosomal protein eL29 /


Mass: 8041.588 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: C6S3J6
#32: Protein/peptide 60S ribosomal protein uL30 /


Mass: 30593.184 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: O97250
#33: Protein/peptide 60S ribosomal protein eL30 /


Mass: 11794.760 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IJK8
#34: Protein/peptide 60S ribosomal protein eL31 /


Mass: 14099.854 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8I463
#35: Protein/peptide 60S ribosomal protein eL32 /


Mass: 15565.751 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8I3B0
#36: Protein/peptide 60S ribosomal protein eL33 /


Mass: 16306.425 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IHT9
#37: Protein/peptide 60S ribosomal protein eL34 /


Mass: 17406.967 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IBY4
#38: Protein/peptide 60S ribosomal protein eL36 /


Mass: 12825.440 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8I713
#39: Protein/peptide 60S ribosomal protein eL37 /


Mass: 10571.592 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: C0H4L5
#40: Protein/peptide 60S ribosomal protein eL38 /


Mass: 10341.729 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8II62
#41: Protein/peptide 60S ribosomal protein eL39 /


Mass: 6540.912 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: C0H4H3
#42: Protein/peptide 60S ribosomal protein eL40 /


Mass: 14645.169 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8ID50
#43: Protein/peptide 60S ribosomal protein eL41 /


Mass: 5108.310 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: C6S3G4
#44: Protein/peptide 60S ribosomal protein eL43 /


Mass: 10826.083 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: O96184
#45: Protein/peptide 60S ribosomal protein eL44 /


Mass: 12194.902 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: O97231

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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 / Magnesium
#47: Chemical
ChemComp-ZN / ZINC ION


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

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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: Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine
Type: RIBOSOME
Molecular weightValue: 4.2 MDa / 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 FIELDBright-field microscopy / 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[at]mrc-lmb.cam.ac.uk
Description: (un)restrained refinement or idealisation of macromolecular structures
EM software
IDNameVersionCategory
1CTFFIND3CTF correction
2RELION3D reconstruction
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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