3J7A

Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine, small subunit


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.2 Å
  • Aggregation State: Particle
  • Reconstruction Method: Single Particle

Literature

Macromolecules
Sequence Display for 3J7A

Classification: RIBOSOME / INHIBITOR

Total Structure Weight: 1263059.88


Macromolecule Entities
Molecule Chains Length Organism Details
40S ribosomal protein eS1 B 262 Plasmodium falciparum Gene Name(s): MAL3P7.35 PFC1020c
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein uS2 C 263 Plasmodium falciparum Gene Name(s): PF10_0264
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein uS3 D 221 Plasmodium falciparum Gene Name(s): PF14_0627
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein uS4 E 189 Plasmodium falciparum Gene Name(s): PFE1005w
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein eS4 F 261 Plasmodium falciparum Gene Name(s): PF11_0065
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein uS5 G 272 Plasmodium falciparum Gene Name(s): PF14_0448
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein eS6 H 306 Plasmodium falciparum Gene Name(s): PF13_0228
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein uS7 I 195 Plasmodium falciparum Gene Name(s): PF07_0088
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein eS7 J 194 Plasmodium falciparum Gene Name(s): PF13_0014
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein uS8 K 130 Plasmodium falciparum Gene Name(s): PFC0735w
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein eS8 L 218 Plasmodium falciparum Gene Name(s): PF14_0083
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein uS9 M 144 Plasmodium falciparum Gene Name(s): PF08_0076
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein uS10 N 118 Plasmodium falciparum Gene Name(s): PF10_0038
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein eS10 O 137 Plasmodium falciparum Gene Name(s): PF07_0080
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein uS11 P 151 Plasmodium falciparum Gene Name(s): PFE0810c
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein uS12 Q 145 Plasmodium falciparum Gene Name(s): PFC0290w
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein eS12 R 141 Plasmodium falciparum Gene Name(s): RPS12 Gene View MAL3P2.28 PFC0295C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein uS13 S 156 Plasmodium falciparum Gene Name(s): PF11_0272
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein uS14 T 54 Plasmodium falciparum Gene Name(s): MAL7P1.300
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein uS15 U 151 Plasmodium falciparum Gene Name(s): PF13_0316
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein uS17 V 161 Plasmodium falciparum Gene Name(s): PFC0775w
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein eS17 W 137 Plasmodium falciparum Gene Name(s): PFL2055w
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein uS19 X 145 Plasmodium falciparum Gene Name(s): MAL13P1.92
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein eS19 Y 170 Plasmodium falciparum Gene Name(s): PFD1055w
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein eS21 Z 82 Plasmodium falciparum Gene Name(s): PF11_0454
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein eS24 1 133 Plasmodium falciparum Gene Name(s): PFE0975c
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein eS25 2 105 Plasmodium falciparum Gene Name(s): PF14_0205
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein eS26 3 107 Plasmodium falciparum Gene Name(s): PFB0830w
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein eS27 4 82 Plasmodium falciparum Gene Name(s): PF13_0045
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein eS28 5 67 Plasmodium falciparum Gene Name(s): PF14_0585
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein eS30 6 58 Plasmodium falciparum Gene Name(s): RPS30 PFB0885w
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
18S ribosomal RNA A 2092 Plasmodium falciparum
tRNA 7 74 Plasmodium falciparum

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
34G
Query on 34G

A emetine
7', (Synonym)
C29 H40 N2 O4
AUVVAXYIELKVAI-TXQMCKRASA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

T ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.2 Å
  • Reconstruction Method: Single Particle

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2014-06-03
  • Released Date: 2014-07-16
  • Deposition author(s): Wong, W., Bai, X.C., Brown, A., Fernandez, I.S., Hanssen, E., Condron, M., Tan, Y.H., Baum, J., Scheres, S.H.W.

Revision History

  • 2015-04-08
    Type: Structure summary
  • 2015-06-03
    Type: Database references