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- PDB-3j79: Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound... -

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Basic information

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 / 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 from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / 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 / cytosolic large ribosomal subunit / cytoplasmic translation / 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 protein L22e / Ribosomal protein L22e superfamily / Ribosomal L38e protein family / Ribosomal L22e 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 L30/YlxQ / Ribosomal protein L13e / Ribosomal protein L13e / 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. / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L7, eukaryotic / Ribosomal protein L6e / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / 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 L14e domain / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L30e signature 2. / 60S ribosomal protein L19 / Ribosomal protein L32e, conserved site / 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 L14 / Ribosomal protein L39e signature. / Ribosomal protein L21e / Ribosomal_L15e / Ribosomal protein L15e / Ribosomal protein L15e core domain superfamily / Ribosomal protein L14 / Ribosomal protein L31e / Ribosomal protein L37ae/L37e / Ribosomal protein L14, KOW motif / Ribosomal protein L24e-related / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein L24e/L24 superfamily / 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
Similarity search - Domain/homology
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 ...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 / 60S ribosomal protein L34 / 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 (malaria parasite P. falciparum)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
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 /
Abstract: Malaria inflicts an enormous burden on global human health. The emergence of parasite resistance to front-line drugs has prompted a renewed focus on the repositioning of clinically approved drugs as ...Malaria inflicts an enormous burden on global human health. The emergence of parasite resistance to front-line drugs has prompted a renewed focus on the repositioning of clinically approved drugs as potential anti-malarial therapies. Antibiotics that inhibit protein translation are promising candidates for repositioning. We have solved the cryo-EM structure of the cytoplasmic ribosome from the human malaria parasite, Plasmodium falciparum, in complex with emetine at 3.2 Å resolution. Emetine is an anti-protozoan drug used in the treatment of ameobiasis that also displays potent anti-malarial activity. Emetine interacts with the E-site of the ribosomal small subunit and shares a similar binding site with the antibiotic pactamycin, thereby delivering its therapeutic effect by blocking mRNA/tRNA translocation. As the first cryo-EM structure that visualizes an antibiotic bound to any ribosome at atomic resolution, this establishes cryo-EM as a powerful tool for screening and guiding the design of drugs that target parasite translation machinery.
History
DepositionJun 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 1VX6, 1VX7
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Dec 17, 2014Group: Other
Revision 1.3Jun 3, 2015Group: Database references
Revision 1.4Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

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  • Deposited structure unit
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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
Polymers2,131,60045
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 method: isolated from a natural source
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 method: isolated from a natural source
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 method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7

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

#4: Protein 60S ribosomal protein uL2 /


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


Mass: 14645.169 Da / Num. of mol.: 1 / Source method: isolated from a natural source
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 method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / References: UniProt: C6S3G4
#44: Protein 60S ribosomal protein eL43 /


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


Mass: 12194.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source
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 / Source method: obtained synthetically / Formula: Mg
#47: 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 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
pH: 7.4
Details: 20 mM HEPES, pH 7.4, 40 mM potassium acetate, 10 mM ammonium acetate, 10 mM magnesium acetate, 5 mM BME
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
MicroscopyModel: 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 X / Calibrated magnification: 104748 X / Nominal defocus max: 3800 nm / Nominal defocus min: 800 nm / Cs: 2 mm
Specimen holderSpecimen holder type: GATAN LIQUID NITROGEN / Temperature: 85 K / Temperature (max): 90 K / Temperature (min): 80 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Details: An in-house system was used to intercept videos from the detector at a rate of 17 frames/second (1 second exposures).
Image scansNum. 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 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 105247 / Nominal pixel size: 1.34 Å / Actual pixel size: 1.34 Å
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
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms50662 73684 168 0 124514

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