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- PDB-6okk: Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound... -

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Entry
Database: PDB / ID: 6okk
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
  • E-site tRNA
Keywordsribosome/inhibitor / Protein synthesis / antimalarial drug / RIBOSOME / ribosome-inhibitor complex
Function / homology
Function and homology information


Ub-specific processing proteases / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Negative regulators of DDX58/IFIH1 signaling / Protein methylation / GTP hydrolysis and joining of the 60S ribosomal subunit / Ribosomal scanning and start codon recognition / Formation of the ternary complex, and subsequently, the 43S complex / Formation of a pool of free 40S subunits / RMTs methylate histone arginines ...Ub-specific processing proteases / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Negative regulators of DDX58/IFIH1 signaling / Protein methylation / GTP hydrolysis and joining of the 60S ribosomal subunit / Ribosomal scanning and start codon recognition / Formation of the ternary complex, and subsequently, the 43S complex / Formation of a pool of free 40S subunits / RMTs methylate histone arginines / SRP-dependent cotranslational protein targeting to membrane / mTORC1-mediated signalling / L13a-mediated translational silencing of Ceruloplasmin expression / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / oxidized purine DNA binding / 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) / maturation of SSU-rRNA / oxidized purine nucleobase lesion DNA N-glycosylase activity / positive regulation of translational fidelity / small-subunit processome / ribosomal small subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytoplasmic translation / positive regulation of DNA repair / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / DNA-(apurinic or apyrimidinic site) endonuclease activity / mRNA 5'-UTR binding / small ribosomal subunit / rRNA processing / cytosolic small ribosomal subunit / ribosome / rRNA binding / structural constituent of ribosome / damaged DNA binding / translation / mRNA binding / DNA repair / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleus / cytosol
Winged helix DNA-binding domain superfamily / Ribosomal protein S21e superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S11 superfamily / RNA-binding S4 domain superfamily / 40S Ribosomal protein S10 / Ribosomal protein S19e domain superfamily / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S26e superfamily ...Winged helix DNA-binding domain superfamily / Ribosomal protein S21e superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S11 superfamily / RNA-binding S4 domain superfamily / 40S Ribosomal protein S10 / Ribosomal protein S19e domain superfamily / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S26e superfamily / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S17e-like superfamily / Ribosomal protein S4, KOW domain / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S12/S23 / Ribosomal protein S7p/S5e / Ribosomal protein S3, C-terminal domain / Ribosomal protein S19 / Ribosomal protein S14p/S29e / Ribosomal protein S15 / Ribosomal protein S3, C-terminal domain superfamily / Winged helix-like DNA-binding domain superfamily / Ribosomal protein S5, N-terminal domain / Ribosomal protein S2, flavodoxin-like domain superfamily / 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 S8e/ribosomal biogenesis NSA2 / Ribosomal protein S4/S9 / Ribosomal protein S15P / Ribosomal protein S19, superfamily / Ribosomal protein S7 domain / Ribosomal protein S8 superfamily / 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 S28e conserved site / 50S ribosomal protein L30e-like / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal / Ribosomal protein S2 / Ribosomal protein S10p/S20e / Ribosomal protein S19e, conserved site / Ribosomal protein S9 signature. / RS4NT (NUC023) domain / 40S ribosomal protein S4 C-terminus / Ribosomal_S17 N-terminal / Ribosomal protein S7 signature. / Ribosomal protein S8 signature. / Ribosomal protein S11 signature. / Ribosomal protein S12 signature. / Ribosomal protein S17 signature. / Ribosomal protein S19 signature. / Ribosomal protein S14 signature. / KH domain / Ribosomal protein S4e signature. / Ribosomal protein S24e signature. / Ribosomal protein S6e signature. / Ribosomal protein S19e signature. / Ribosomal protein S4 signature. / Ribosomal protein S13 signature. / Ribosomal protein S17e signature. / Ribosomal protein S26e signature. / Ribosomal protein S28e signature. / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S30 / Ribosomal protein S17 / Ribosomal protein S28e / Ribosomal protein S9/S16 / Ribosomal protein S8 / Ribosomal protein S11 / Ribosomal protein S13/S18 / Ribosomal S17 / Ribosomal family S4e / Ribosomal S3Ae family / Ribosomal protein S19e / Ribosomal protein S6e / Ribosomal protein S8e / Ribosomal protein S5, C-terminal domain / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein S21e / Ribosomal protein S7e / Ribosomal protein S24e / Ribosomal protein S26e / S4 domain / Ribosomal protein S27 / S25 ribosomal protein / Plectin/S10 domain / Ribosomal protein S6e, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S2 signature 2. / Ribosomal protein S26e / Ribosomal protein S7e / Ribosomal protein S15 / Ribosomal protein S27e
40S ribosomal protein S27 / 40S ribosomal protein S7 / 40S ribosomal protein S19 / 40S ribosomal protein S21 / 40S ribosomal protein S18, putative / 40S ribosomal protein S4 / 40S ribosomal protein SA / 40S ribosomal protein S15 / 40S ribosomal protein S20e, putative / 40S ribosomal protein S3 ...40S ribosomal protein S27 / 40S ribosomal protein S7 / 40S ribosomal protein S19 / 40S ribosomal protein S21 / 40S ribosomal protein S18, putative / 40S ribosomal protein S4 / 40S ribosomal protein SA / 40S ribosomal protein S15 / 40S ribosomal protein S20e, putative / 40S ribosomal protein S3 / 40S ribosomal protein S28e, putative / 40S ribosomal protein S5 / 40S ribosomal protein S25 / 40S ribosomal protein S6 / 40S ribosomal protein S30 / 40S ribosomal protein S10, putative / 40S ribosomal protein S5, putative / 40S ribosomal protein S17, putative / 40S ribosomal protein S11 / 40S ribosomal protein S24 / 40S ribosomal protein S9, putative / 40S ribosomal protein S3a / 40S ribosomal protein S12 / 40S ribosomal protein S23, putative / 40S ribosomal protein S26 / 40S ribosomal protein S15A, putative / 40S ribosomal protein S11, putative / 40S ribosomal protein S19 / 40S ribosomal protein S29, putative / 40S ribosomal protein S16 / 40S ribosomal protein S8
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsWong, W. / Scheres, S.H.W.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (Australia)APP1053801, APP1024678 Australia
CitationJournal: To Be Published
Title: Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine.
Authors: Wong, W. / Schere, S.H.W.
Validation Report
SummaryFull reportAbout validation report
History
DepositionApr 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2019Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: 18S ribosomal RNA
B: 40S ribosomal protein S3a
C: 40S ribosomal protein SA
D: 40S ribosomal protein S3
E: 40S ribosomal protein S9
F: 40S ribosomal protein S4
G: 40S ribosomal protein S5
H: 40S ribosomal protein S6
I: 40S ribosomal protein S5
J: 40S ribosomal protein S7
K: 40S ribosomal protein S15A
L: 40S ribosomal protein S8
M: 40S ribosomal protein S16
N: 40S ribosomal protein S20e
O: 40S ribosomal protein S10
P: 40S ribosomal protein S11
Q: 40S ribosomal protein S23
R: 40S ribosomal protein S12
S: 40S ribosomal protein S18
T: 40S ribosomal protein S29
U: 40S ribosomal protein S15
V: 40S ribosomal protein S11
W: 40S ribosomal protein S17
X: 40S ribosomal protein S19
Y: 40S ribosomal protein S19
Z: 40S ribosomal protein S21
a: 40S ribosomal protein S24
b: 40S ribosomal protein S25
c: 40S ribosomal protein S26
d: 40S ribosomal protein S27
e: 40S ribosomal protein S28e
f: 40S ribosomal protein S30
g: E-site tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,263,060102
Polymers1,260,88533
Non-polymers2,17469
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 2 types, 2 molecules Ag

#1: RNA chain 18S ribosomal RNA /


Mass: 671337.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7
#33: RNA chain E-site tRNA


Mass: 23774.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7

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

#2: Protein/peptide 40S ribosomal protein S3a /


Mass: 30111.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: O97313
#3: Protein/peptide 40S ribosomal protein SA /


Mass: 29891.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: Q8IJD4
#4: Protein/peptide 40S ribosomal protein S3 /


Mass: 24709.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: Q8IKH8
#5: Protein/peptide 40S ribosomal protein S9 /


Mass: 22172.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: Q8I3R0
#6: Protein/peptide 40S ribosomal protein S4 /


Mass: 29830.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: Q8IIU8
#7: Protein/peptide 40S ribosomal protein S5 /


Mass: 30008.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: Q8IL02
#8: Protein/peptide 40S ribosomal protein S6 /


Mass: 35473.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: Q8IDR9
#9: Protein/peptide 40S ribosomal protein S5 /


Mass: 21898.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: Q8IBN5
#10: Protein/peptide 40S ribosomal protein S7 /


Mass: 22524.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: Q8IET7
#11: Protein/peptide 40S ribosomal protein S15A /


Mass: 14900.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: O77395
#12: Protein/peptide 40S ribosomal protein S8 /


Mass: 25105.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: Q8IM10
#13: Protein/peptide 40S ribosomal protein S16 /


Mass: 16318.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: A0A0L7M7C8
#14: Protein/peptide 40S ribosomal protein S20e / Ribosome


Mass: 13534.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: Q8IK02
#15: Protein/peptide 40S ribosomal protein S10 /


Mass: 16510.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: Q8IBQ5
#16: Protein/peptide 40S ribosomal protein S11 /


Mass: 16105.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: Q8I3U6
#17: Protein/peptide 40S ribosomal protein S23 /


Mass: 16166.962 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: O97248
#18: Protein/peptide 40S ribosomal protein S12 /


Mass: 15414.444 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: O97249
#19: Protein/peptide 40S ribosomal protein S18 /


Mass: 17928.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: Q8IIA2
#20: Protein/peptide 40S ribosomal protein S29 /


Mass: 6430.679 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: C0H4K8
#21: Protein/peptide 40S ribosomal protein S15 /


Mass: 17286.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: Q8IDB0
#22: Protein/peptide 40S ribosomal protein S11 /


Mass: 18801.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: O77381
#23: Protein/peptide 40S ribosomal protein S17 /


Mass: 16096.985 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: Q8I502
#24: Protein/peptide 40S ribosomal protein S19 /


Mass: 16800.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: C0H5C2
#25: Protein/peptide 40S ribosomal protein S19 /


Mass: 19757.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: Q8IFP2
#26: Protein/peptide 40S ribosomal protein S21 /


Mass: 9157.478 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: Q8IHS5
#27: Protein/peptide 40S ribosomal protein S24 /


Mass: 15431.478 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: Q8I3R6
#28: Protein/peptide 40S ribosomal protein S25 /


Mass: 11691.931 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: Q8ILN8
#29: Protein/peptide 40S ribosomal protein S26 /


Mass: 12539.681 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: O96258
#30: Protein/peptide 40S ribosomal protein S27 /


Mass: 9154.856 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: Q8IEN2
#31: Protein/peptide 40S ribosomal protein S28e / Ribosome


Mass: 7508.800 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / References: UniProt: Q8IKL9
#32: Protein/peptide 40S ribosomal protein S30 /


Mass: 6508.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 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 / Source method: obtained synthetically / Formula: Mg / Magnesium
#35: Chemical ChemComp-34G / emetine / (3beta,14beta)-6',7',10,11-tetramethoxyemetan


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


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Zinc

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine, small subunit
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
Source: NATURAL
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote)
Buffer solutionpH: 7.2
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: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameCategory
4RELIONCTF correction
7UCSF Chimeramodel fitting
13REFMACmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 105247 / Symmetry type: POINT
RefinementHighest resolution: 3.3 Å

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