3J79

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


Experimental Data Snapshot

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

Literature

Macromolecules
Sequence Display for 3J79

Classification: RIBOSOME / INHIBITOR

Total Structure Weight: 2135888.75


Macromolecule Entities
Molecule Chains Length Organism Details
60S ribosomal protein uL2 D 260 Plasmodium falciparum Gene Name(s): PFE0845c
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein uL3 E 386 Plasmodium falciparum Gene Name(s): PF10_0272
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein uL4 F 411 Plasmodium falciparum Gene Name(s): PFE0350c
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein uL5 G 173 Plasmodium falciparum Gene Name(s): PF07_0079
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein uL6 H 190 Plasmodium falciparum Gene Name(s): PF13_0129
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein eL6 I 221 Plasmodium falciparum Gene Name(s): PF13_0213
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein eL8 J 283 Plasmodium falciparum Gene Name(s): PF14_0231
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein uL13 K 202 Plasmodium falciparum Gene Name(s): PF10_0043
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein eL13 L 215 Plasmodium falciparum Gene Name(s): PF08_0075
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein uL14 M 139 Plasmodium falciparum Gene Name(s): PF13_0171
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein eL14 N 165 Plasmodium falciparum Gene Name(s): PF14_0296
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein uL15 O 148 Plasmodium falciparum Gene Name(s): PFF0885w
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein eL15 P 205 Plasmodium falciparum Gene Name(s): PFD0770c
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein uL16 Q 219 Plasmodium falciparum Gene Name(s): PF14_0141
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein uL18 R 294 Plasmodium falciparum Gene Name(s): PF14_0230
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein eL18 S 187 Plasmodium falciparum Gene Name(s): MAL13P1.209
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein eL19 T 182 Plasmodium falciparum Gene Name(s): PFF0700c
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein eL20 U 184 Plasmodium falciparum Gene Name(s): PF13_0224
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein eL21 V 161 Plasmodium falciparum Gene Name(s): PF14_0240
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein uL22 W 203 Plasmodium falciparum Gene Name(s): PF13_0268
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein eL22 X 139 Plasmodium falciparum Gene Name(s): PF08_0039
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein uL23 Y 190 Plasmodium falciparum Gene Name(s): PF13_0132
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein uL24 Z 126 Plasmodium falciparum Gene Name(s): PFC0535w
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein eL24 0 162 Plasmodium falciparum Gene Name(s): PF13_0049
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein eL27 1 146 Plasmodium falciparum Gene Name(s): PF14_0579
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein eL28 2 127 Plasmodium falciparum Gene Name(s): PF11_0437
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein uL29 3 124 Plasmodium falciparum Gene Name(s): PF11_0260
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein eL29 4 67 Plasmodium falciparum Gene Name(s): PF14_0575a
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein uL30 5 257 Plasmodium falciparum Gene Name(s): PFC0300c
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein eL30 6 108 Plasmodium falciparum Gene Name(s): PF10_0187
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein eL31 7 120 Plasmodium falciparum Gene Name(s): PFE0185c
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein eL32 8 131 Plasmodium falciparum Gene Name(s): PFI0190w
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein eL33 9 140 Plasmodium falciparum Gene Name(s): PF11_0438
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein eL34 a 150 Plasmodium falciparum Gene Name(s): PF07_0043
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein eL36 b 112 Plasmodium falciparum Gene Name(s): PF11_0106
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein eL37 c 92 Plasmodium falciparum Gene Name(s): MAL7P1.320
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein eL38 d 87 Plasmodium falciparum Gene Name(s): PF11_0312
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein eL39 e 51 Plasmodium falciparum Gene Name(s): PFF0573c
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein eL40 f 128 Plasmodium falciparum Gene Name(s): PF13_0346
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein eL41 g 39 Plasmodium falciparum Gene Name(s): PF11_0455a
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein eL43 h 96 Plasmodium falciparum Gene Name(s): RPL37A Gene View PFB0455w
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein eL44 i 104 Plasmodium falciparum Gene Name(s): RPL44 MAL3P2.9 PFC0200W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
28S ribosomal RNA A 3788 Plasmodium falciparum
5S ribosomal RNA B 119 Plasmodium falciparum
5.8S ribosomal RNA C 159 Plasmodium falciparum

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

a, c, f, h, i ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, C, M, Q 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



Entry History

Deposition Data

  • Deposited Date: 2014-06-02
  • 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.
  • This entry supercedes: 1VX6 1VX7

Revision History

  • Version 1_0: 2014-07-16

    Type: Initial release

  • Version 1_1: 2014-12-10

    Type: Other

  • Version 1_2: 2014-12-17

    Type: Other

  • Version 1_3: 2015-06-03

    Type: Database references