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- PDB-3j7a: Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound... -

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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
Components
  • (40S ribosomal protein ...) x 31
  • 18S ribosomal RNA
  • tRNATransfer RNA
KeywordsRIBOSOME/INHIBITOR / emetine / RIBOSOME-INHIBITOR complex
Function / homologyRibosomal protein S8 superfamily / 40S Ribosomal protein S10 / Winged helix-like DNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / Ribosomal protein S17e-like superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S11 superfamily / RNA-binding S4 domain superfamily ...Ribosomal protein S8 superfamily / 40S Ribosomal protein S10 / Winged helix-like DNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / Ribosomal protein S17e-like superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S11 superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S19e domain superfamily / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S26e superfamily / Ribosomal protein S21e superfamily / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S12/S23 / Ribosomal protein S7p/S5e / Ribosomal protein S3, C-terminal domain / Ribosomal protein S19 / 40S ribosomal protein S11, N-terminal / 50S ribosomal protein L30e-like / Ribosomal protein S15 / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S17e, conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein S17, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein S4/S9 / Ribosomal protein S28e conserved site / Ribosomal protein S15P / Ribosomal protein S19, superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S7 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein S10 domain / Ribosomal protein S2, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S14p/S29e / Ribosomal protein S2 / Ribosomal protein S13, conserved site / Ribosomal protein S11 signature. / Ribosomal protein S30 / KH domain / Ribosomal S13/S15 N-terminal domain / RS4NT (NUC023) domain / 40S ribosomal protein S4 C-terminus / Ribosomal_S17 N-terminal / Ribosomal protein S7 signature. / Ribosomal protein S8 signature. / Ribosomal protein S12 signature. / Plectin/S10 domain / Ribosomal protein S17 signature. / Ribosomal protein S19 signature. / Ribosomal protein S9 signature. / Ribosomal protein S14 signature. / Ribosomal protein S4e signature. / Ribosomal protein S24e signature. / Ribosomal protein S6e signature. / Ribosomal protein S19e signature. / Ribosomal protein S4 signature. / Ribosomal protein S5, C-terminal domain / S25 ribosomal protein / Ribosomal protein S5, N-terminal domain / Ribosomal S3Ae family / Ribosomal protein S10p/S20e / Ribosomal protein S17 / Ribosomal protein S9/S16 / Ribosomal protein S8 / Ribosomal protein S11 / Ribosomal protein S13/S18 / Ribosomal S17 / Ribosomal family S4e / Ribosomal protein S19e / Ribosomal protein S27 / Ribosomal protein S6e / Ribosomal protein S28e / Ribosomal protein S8e / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein S21e / Ribosomal protein S7e / Ribosomal protein S24e / Ribosomal protein S26e / S4 domain / Ribosomal protein S14, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S5 / Ribosomal protein S28e / Ribosomal protein S12e / Ribosomal protein S7e / Ribosomal protein S15 / Ribosomal protein S27e / Ribosomal protein S8 / Ribosomal protein S9
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 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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Structure visualization

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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 chain 18S ribosomal RNA /


Mass: 671337.500 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7
#33: RNA chain tRNA / Transfer RNA


Mass: 23774.059 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7

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40S ribosomal protein ... , 31 types, 31 molecules BCDEFGHIJKLMNOPQRSTUVWXYZ123456

#2: Protein/peptide 40S ribosomal protein eS1 /


Mass: 30111.678 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: O97313
#3: Protein/peptide 40S ribosomal protein uS2 /


Mass: 29891.182 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IJD4
#4: Protein/peptide 40S ribosomal protein uS3 /


Mass: 24709.908 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IKH8
#5: Protein/peptide 40S ribosomal protein uS4 /


Mass: 22172.076 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8I3R0
#6: Protein/peptide 40S ribosomal protein eS4 /


Mass: 29830.330 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IIU8
#7: Protein/peptide 40S ribosomal protein uS5 /


Mass: 30008.768 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IL02
#8: Protein/peptide 40S ribosomal protein eS6 /


Mass: 35473.766 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IDR9
#9: Protein/peptide 40S ribosomal protein uS7 /


Mass: 21898.484 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IBN5
#10: Protein/peptide 40S ribosomal protein eS7 /


Mass: 22524.740 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IET7
#11: Protein/peptide 40S ribosomal protein uS8 /


Mass: 14900.678 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: O77395
#12: Protein/peptide 40S ribosomal protein eS8 /


Mass: 25105.992 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IM10
#13: Protein/peptide 40S ribosomal protein uS9 /


Mass: 16318.242 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IAX5
#14: Protein/peptide 40S ribosomal protein uS10 /


Mass: 13534.918 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IK02
#15: Protein/peptide 40S ribosomal protein eS10 /


Mass: 16510.201 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IBQ5
#16: Protein/peptide 40S ribosomal protein uS11 /


Mass: 16105.612 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8I3U6
#17: Protein/peptide 40S ribosomal protein uS12 /


Mass: 16166.962 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: O97248
#18: Protein/peptide 40S ribosomal protein eS12 /


Mass: 15414.444 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: O97249
#19: Protein/peptide 40S ribosomal protein uS13 /


Mass: 17928.947 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IIA2
#20: Protein/peptide 40S ribosomal protein uS14 /


Mass: 6430.679 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: C0H4K8
#21: Protein/peptide 40S ribosomal protein uS15 /


Mass: 17286.469 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IDB0
#22: Protein/peptide 40S ribosomal protein uS17 /


Mass: 18801.189 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: O77381
#23: Protein/peptide 40S ribosomal protein eS17 /


Mass: 16096.985 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8I502
#24: Protein/peptide 40S ribosomal protein uS19 /


Mass: 16800.764 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: C0H5C2
#25: Protein/peptide 40S ribosomal protein eS19 /


Mass: 19757.920 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IFP2
#26: Protein/peptide 40S ribosomal protein eS21 /


Mass: 9157.478 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IHS5
#27: Protein/peptide 40S ribosomal protein eS24 /


Mass: 15431.478 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8I3R6
#28: Protein/peptide 40S ribosomal protein eS25 /


Mass: 11691.931 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8ILN8
#29: Protein/peptide 40S ribosomal protein eS26 /


Mass: 12539.681 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: O96258
#30: Protein/peptide 40S ribosomal protein eS27 /


Mass: 9154.856 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IEN2
#31: Protein/peptide 40S ribosomal protein eS28 /


Mass: 7508.800 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: Q8IKL9
#32: Protein/peptide 40S ribosomal protein eS30 /


Mass: 6508.725 Da / Num. of mol.: 1
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: O96269

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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 / Magnesium
#35: Chemical ChemComp-34G / emetine / (3beta,14beta)-6',7',10,11-tetramethoxyemetan


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


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

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