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- PDB-5umd: Structure of the Plasmodium falciparum 80S ribosome bound to the ... -

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Basic information

Entry
Database: PDB / ID: 5umd
TitleStructure of the Plasmodium falciparum 80S ribosome bound to the antimalarial drug mefloquine
Components
  • (60S ribosomal protein ...) x 39
  • (Ribosomal protein ...) x 2
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • Ubiquitin-60S ribosomal protein L40
KeywordsRIBOSOME / protein synthesis / antimalarial
Function / homology
Function and homology information


Translesion synthesis by REV1 / Translesion Synthesis by POLH / : / Translesion synthesis by POLK / Translesion synthesis by POLI / Josephin domain DUBs / : / Metalloprotease DUBs / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / ER Quality Control Compartment (ERQC) ...Translesion synthesis by REV1 / Translesion Synthesis by POLH / : / Translesion synthesis by POLK / Translesion synthesis by POLI / Josephin domain DUBs / : / Metalloprotease DUBs / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / ER Quality Control Compartment (ERQC) / Iron uptake and transport / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Formation of a pool of free 40S subunits / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Aggrephagy / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / : / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / KEAP1-NFE2L2 pathway / UCH proteinases / Ub-specific processing proteases / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / protein-RNA complex assembly / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / modification-dependent protein catabolic process / protein tag activity / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / large ribosomal subunit / ribosome biogenesis / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / ubiquitin-dependent protein catabolic process / negative regulation of translation / rRNA binding / protein ubiquitination / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / ubiquitin protein ligase binding / RNA binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L29e / Ribosomal protein L10e, conserved site / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein L10e / Ribosomal L29e protein family / Ribosomal protein L34e, conserved site / Eukaryotic Ribosomal Protein L27, KOW domain ...Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L29e / Ribosomal protein L10e, conserved site / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein L10e / Ribosomal L29e protein family / Ribosomal protein L34e, conserved site / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L44e / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L38e protein family / Ribosomal protein L23/L25, N-terminal / 60S ribosomal protein L35 / Ribosomal protein L30e, conserved site / Ribosomal protein L44 / Ribosomal protein L34Ae / Ribosomal protein L23, N-terminal domain / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal L27e protein family / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L30/YlxQ / Ribosomal protein L34e / Ribosomal protein L31e, conserved site / Ribosomal protein L37ae / 60S ribosomal protein L6E / Ribosomal protein L19, eukaryotic / Ribosomal protein L35A / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal L40e family / Ribosomal protein L36e / Ribosomal protein L35A superfamily / Ribosomal protein L44e signature. / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L7A/L8 / Ribosomal protein L10e signature. / Ribosomal protein L13e / Ribosomal protein L13e / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L6e / Ribosomal L37ae protein family / Ribosomal protein L35Ae / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L39e, conserved site / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / 60S ribosomal protein L4 C-terminal domain / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L34e signature. / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal_L31e / Ribosomal protein L15e, conserved site / Ribosomal protein L30e signature 1. / Ribosomal protein L21e / Ribosomal protein L21e, conserved site / Ribosomal protein L21 superfamily / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L30e signature 2. / 60S ribosomal protein L19 / Ribosomal protein L37e, conserved site / Ribosomal protein L3, domain 3, archaeal type superfamily / Ribosomal protein L3, archaeal/eukaryotic type / Ribosomal protein L36e signature. / Ribosomal protein L37e / Ribosomal protein L39e signature. / Ribosomal protein L21e / Ribosomal_L15e / Ribosomal protein L15e / Ribosomal protein L15e core domain superfamily / Ribosomal protein L31e / Ribosomal protein L37ae/L37e / Ribosomal protein L24e-related / Ribosomal protein L7, eukaryotic / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L39e / Ribosomal protein L26/L24, eukaryotic/archaeal / Ribosomal protein L39e domain superfamily / Ribosomal_L19e / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L4, eukaryotic and archaeal type
Similarity search - Domain/homology
Mefloquine / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosomal protein L15 / 60S ribosomal protein L39 ...Mefloquine / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Ribosomal protein L15 / 60S ribosomal protein L39 / Ribosomal protein L37 / 60S ribosomal protein L18-2, putative / 60S ribosomal protein L19 / 60S ribosomal protein L27a, putative / 60S ribosomal protein L41 / 60S ribosomal protein L29 / 60S ribosomal protein L26, putative / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL42 / 60S ribosomal protein L7, putative / 60S ribosomal protein L32 / 60S ribosomal protein L2 / 60S ribosomal protein L4 / 60S ribosomal protein L31 / 60S ribosomal protein L36 / 60S ribosomal protein L13 / Large ribosomal subunit protein eL22 / 60S ribosomal protein L11a, putative / Large ribosomal subunit protein eL34 / Ubiquitin-60S ribosomal protein L40 / 60S ribosomal protein L17, putative / 60S ribosomal protein L18a / 60S ribosomal protein L6-2, putative / 60S ribosomal protein L23, putative / 60S ribosomal protein L23 / 60S ribosomal protein L6, putative / 60S ribosomal protein L24, putative / 60S ribosomal protein L35ae, putative / 60S ribosomal protein L28 / 60S ribosomal protein L38 / 60S ribosomal protein L35, putative / 60S ribosomal protein L3 / 60S ribosomal protein L30e, putative / 60S ribosomal protein L13, putative / 60S ribosomal protein L27 / 60S ribosomal protein L14, putative / 60S ribosomal protein L21 / 60S ribosomal protein L7a / 60S ribosomal protein L5, putative / 60S ribosomal protein L10, putative
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsWong, W. / Bai, X.-C. / Brown, A. / Scheres, S. / Baum, J.
Funding support Australia, United Kingdom, 8items
OrganizationGrant numberCountry
NHMRCAPP1024678 Australia
NHMRCAPP1053801 Australia
Medical Research Council (United Kingdom)MC_UP_A025_1013 United Kingdom
Medical Research Council (United Kingdom)MC_U105184332 United Kingdom
Wellcome TrustWT096570 United Kingdom
Wellcome Trust100993/Z/13/Z United Kingdom
Human Frontier Science ProgramRGY0071/2011 United Kingdom
Department of Industry, Innovation, Science, Research and Tertiary Education, Australian Government|Australian Research CouncilFT100100112 Australia
CitationJournal: Nat Microbiol / Year: 2017
Title: Mefloquine targets the Plasmodium falciparum 80S ribosome to inhibit protein synthesis.
Authors: Wilson Wong / Xiao-Chen Bai / Brad E Sleebs / Tony Triglia / Alan Brown / Jennifer K Thompson / Katherine E Jackson / Eric Hanssen / Danushka S Marapana / Israel S Fernandez / Stuart A Ralph ...Authors: Wilson Wong / Xiao-Chen Bai / Brad E Sleebs / Tony Triglia / Alan Brown / Jennifer K Thompson / Katherine E Jackson / Eric Hanssen / Danushka S Marapana / Israel S Fernandez / Stuart A Ralph / Alan F Cowman / Sjors H W Scheres / Jake Baum /
Abstract: Malaria control is heavily dependent on chemotherapeutic agents for disease prevention and drug treatment. Defining the mechanism of action for licensed drugs, for which no target is characterized, ...Malaria control is heavily dependent on chemotherapeutic agents for disease prevention and drug treatment. Defining the mechanism of action for licensed drugs, for which no target is characterized, is critical to the development of their second-generation derivatives to improve drug potency towards inhibition of their molecular targets. Mefloquine is a widely used antimalarial without a known mode of action. Here, we demonstrate that mefloquine is a protein synthesis inhibitor. We solved a 3.2 Å cryo-electron microscopy structure of the Plasmodium falciparum 80S ribosome with the (+)-mefloquine enantiomer bound to the ribosome GTPase-associated centre. Mutagenesis of mefloquine-binding residues generates parasites with increased resistance, confirming the parasite-killing mechanism. Furthermore, structure-guided derivatives with an altered piperidine group, predicted to improve binding, show enhanced parasiticidal effect. These data reveal one possible mode of action for mefloquine and demonstrate the vast potential of cryo-electron microscopy to guide the development of mefloquine derivatives to inhibit parasite protein synthesis.
History
DepositionJan 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Data collection / Category: em_software / pdbx_audit_support
Item: _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.3Oct 17, 2018Group: Data collection / Refinement description / Category: refine
Revision 1.4Dec 11, 2019Group: Advisory / Derived calculations / Other
Category: atom_sites / pdbx_validate_close_contact ...atom_sites / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3]

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Structure visualization

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  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
A: 28S ribosomal RNA
B: 5S ribosomal RNA
C: 5.8S ribosomal RNA
D: 60S ribosomal protein L2
E: 60S ribosomal protein L3
F: 60S ribosomal protein L4
G: 60S ribosomal protein L11a, putative
H: 60S ribosomal protein L6, putative
I: 60S ribosomal protein L6-2, putative
J: 60S ribosomal protein L7-3, putative
K: 60S ribosomal protein L13, putative
L: 60S ribosomal protein L13
M: 60S ribosomal protein L23, putative
N: 60S ribosomal protein L14, putative
O: 60S ribosomal protein L27a, putative
P: Ribosomal protein L15
Q: 60S ribosomal protein L10, putative
R: 60S ribosomal protein L5, putative
S: 60S ribosomal protein L18-2, putative
T: 60S ribosomal protein L19
U: 60S ribosomal protein L18a
V: 60S ribosomal protein L21
W: 60S ribosomal protein L17, putative
X: 60S ribosomal protein L22, putative
Y: 60S ribosomal protein L23
Z: 60S ribosomal protein L26, putative
0: 60S ribosomal protein L24, putative
1: 60S ribosomal protein L27
2: 60S ribosomal protein L28
3: 60S ribosomal protein L35, putative
4: 60S ribosomal protein L29, putative
5: 60S ribosomal protein L7, putative
6: 60S ribosomal protein L30e, putative
7: 60S ribosomal protein L31
8: 60S ribosomal protein L32
9: 60S ribosomal protein L35Ae, putative
a: 60S ribosomal protein L34
b: 60S ribosomal protein L36
c: Ribosomal protein L37
d: 60S ribosomal protein L38
e: 60S ribosomal protein L39
f: Ubiquitin-60S ribosomal protein L40
g: 60S ribosomal protein L41
h: 60S ribosomal protein L37a
i: 60S ribosomal protein L44
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,136,616216
Polymers2,131,54645
Non-polymers5,070171
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area406610 Å2
ΔGint-4819 kcal/mol
Surface area581500 Å2
MethodPISA

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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 method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: GenBank: 1013064538
#2: RNA chain 5S ribosomal RNA /


Mass: 38410.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: GenBank: 1016052399
#3: RNA chain 5.8S ribosomal RNA /


Mass: 51206.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: GenBank: 1013064403

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60S ribosomal protein ... , 39 types, 39 molecules DEFGHIJKLMNOQRSTUVWXYZ01234567...

#4: Protein 60S ribosomal protein L2 /


Mass: 28064.998 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8I3T9
#5: Protein 60S ribosomal protein L3 / / 60S ribosomal protein L3 / putative


Mass: 44318.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IJC6
#6: Protein 60S ribosomal protein L4 /


Mass: 46311.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8I431
#7: Protein 60S ribosomal protein L11a, putative / Ribosome


Mass: 20268.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IBQ6
#8: Protein 60S ribosomal protein L6, putative / Ribosome


Mass: 21638.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IE85
#9: Protein 60S ribosomal protein L6-2, putative / Ribosome


Mass: 25587.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IDV1
#10: Protein 60S ribosomal protein L7-3, putative / Ribosome


Mass: 32760.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8ILL2
#11: Protein 60S ribosomal protein L13, putative / Ribosome


Mass: 23805.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IJZ7
#12: Protein 60S ribosomal protein L13 /


Mass: 25454.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IAX6
#13: Protein 60S ribosomal protein L23, putative / Ribosome


Mass: 15015.713 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IE09
#14: Protein 60S ribosomal protein L14, putative / Ribosome


Mass: 19340.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8ILE8
#15: Protein 60S ribosomal protein L27a, putative / Ribosome


Mass: 16765.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: C6KT23
#17: Protein 60S ribosomal protein L10, putative / Ribosome


Mass: 25265.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8ILV2
#18: Protein 60S ribosomal protein L5, putative / Ribosome


Mass: 34067.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8ILL3
#19: Protein 60S ribosomal protein L18-2, putative / Ribosome


Mass: 21508.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: C0H5G3
#20: Protein 60S ribosomal protein L19 /


Mass: 21641.096 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: C6KSY6
#21: Protein 60S ribosomal protein L18a /


Mass: 21793.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IDS6
#22: Protein 60S ribosomal protein L21 / / 60S ribosomal protein L21e / putative


Mass: 18840.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8ILK3
#23: Protein 60S ribosomal protein L17, putative / Ribosome


Mass: 23469.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IDI5
#24: Protein 60S ribosomal protein L22, putative / Ribosome


Mass: 16422.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IB51
#25: Protein 60S ribosomal protein L23 /


Mass: 22152.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IE82
#26: Protein 60S ribosomal protein L26, putative / Ribosome


Mass: 14855.709 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: O77364
#27: Protein 60S ribosomal protein L24, putative / Ribosome


Mass: 19295.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IEM3
#28: Protein 60S ribosomal protein L27 / / 60S ribosomal protein L27 / putative


Mass: 16785.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IKM5
#29: Protein 60S ribosomal protein L28 / / 60S ribosomal protein L28 / putative


Mass: 14437.823 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IHU0
#30: Protein 60S ribosomal protein L35, putative / Ribosome


Mass: 14787.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IIB4
#31: Protein 60S ribosomal protein L29, putative / Ribosome / Ribosomal protein L29 / putative


Mass: 8041.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: C6S3J6
#32: Protein 60S ribosomal protein L7, putative / Ribosome


Mass: 30593.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: O97250
#33: Protein 60S ribosomal protein L30e, putative / Ribosome


Mass: 11794.760 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IJK8
#34: Protein 60S ribosomal protein L31 /


Mass: 14099.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8I463
#35: Protein 60S ribosomal protein L32 /


Mass: 15565.751 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8I3B0
#36: Protein 60S ribosomal protein L35Ae, putative / Ribosome / 60S ribosomal protein L35ae / putative


Mass: 16306.425 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IHT9
#37: Protein 60S ribosomal protein L34 /


Mass: 17406.967 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8IBY4
#38: Protein 60S ribosomal protein L36 /


Mass: 12825.440 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8I713
#40: Protein 60S ribosomal protein L38 / / 60S ribosomal protein L38e / putative


Mass: 10341.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8II62
#41: Protein 60S ribosomal protein L39 /


Mass: 6540.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: C0H4H3
#43: Protein/peptide 60S ribosomal protein L41 / / 60S ribosomal protein L41 / putative


Mass: 5108.310 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: C6S3G4
#44: Protein 60S ribosomal protein L37a /


Mass: 10826.083 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: O96184
#45: Protein 60S ribosomal protein L44 /


Mass: 12194.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: O97231

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Ribosomal protein ... , 2 types, 2 molecules Pc

#16: Protein Ribosomal protein L15 /


Mass: 24197.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: C0H4A6
#39: Protein Ribosomal protein L37 /


Mass: 10571.592 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: C0H4L5

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Protein , 1 types, 1 molecules f

#42: Protein Ubiquitin-60S ribosomal protein L40


Mass: 14645.169 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Plasmodium falciparum 3D7 (eukaryote) / References: UniProt: Q8ID50

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Non-polymers , 3 types, 171 molecules

#46: Chemical ChemComp-YMZ / Mefloquine / Mefloquine


Mass: 378.312 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H16F6N2O / Comment: medication*YM
#47: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 164 / Source method: obtained synthetically / Formula: Mg
#48: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn

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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 mefloquine
Type: RIBOSOME / Entity ID: #1-#45 / Source: NATURAL
Molecular weightValue: 4.2 MDa / Experimental value: NO
Source (natural)Organism: Plasmodium falciparum 3D7 (eukaryote) / Cellular location: cytoplasm
Buffer solutionpH: 7.4
Details: 20 mM Hepes pH 7.4, 40 mM KAc, 10 mM NH4Ac, 10 mM Mg(Ac)2 and 5 mM 2-mecaptoethanol
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Blot 2.5s before plunging / Grid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 90 K

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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 / Nominal magnification: 78000 X / Calibrated magnification: 104748 X / Calibrated defocus min: 800 nm / Calibrated defocus max: 3800 nm / Cs: 2 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: GATAN LIQUID NITROGEN / Temperature (max): 90 K / Temperature (min): 80 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1
Image scansMovie frames/image: 17

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Processing

SoftwareName: REFMAC / Version: 5.8.0068 / Classification: refinement
EM software
IDNameVersionCategory
2RELION1.3image acquisition
4CTFFIND3CTF correction
7UCSF Chimeramodel fitting
9RELION1.3initial Euler assignment
10RELION1.3final Euler assignment
11RELION1.3classification
12RELION1.33D reconstruction
13REFMAC5.8model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43184 / Symmetry type: POINT
Atomic model buildingB value: 129.3 / Protocol: RIGID BODY FIT / Space: RECIPROCAL
RefinementResolution: 3.2→257.5 Å / Cor.coef. Fo:Fc: 0.952 / SU B: 29.102 / SU ML: 0.428 / ESU R: 0.567
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflection
Rwork0.27921 --
obs0.27921 806977 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 129.307 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20.09 Å20.15 Å2
2--0.17 Å2-0.02 Å2
3---0.08 Å2
Refinement stepCycle: 1 / Total: 124503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0050.014136485
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg0.8751.526196987
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg24.1856.9827685
ELECTRON MICROSCOPYr_dihedral_angle_2_deg33.18621.8972119
ELECTRON MICROSCOPYr_dihedral_angle_3_deg17.8421510690
ELECTRON MICROSCOPYr_dihedral_angle_4_deg11.95715538
ELECTRON MICROSCOPYr_chiral_restr0.3390.21322289
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.0272478
ELECTRON MICROSCOPYr_gen_planes_other
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it1.34413.26824887
ELECTRON MICROSCOPYr_mcbond_other
ELECTRON MICROSCOPYr_mcangle_it2.49619.89131002
ELECTRON MICROSCOPYr_mcangle_other
ELECTRON MICROSCOPYr_scbond_it1.1912.811111598
ELECTRON MICROSCOPYr_scbond_other
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other
ELECTRON MICROSCOPYr_long_range_B_refined7.98518007
ELECTRON MICROSCOPYr_long_range_B_other
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.576 59775 -
Rfree-0 -
obs--100 %

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