3J7A Ribosome Inhibitor date Jun 03, 2014
title Cryo-Em Structure Of The Plasmodium Falciparum 80s Ribosome The Anti-Protozoan Drug Emetine, Small Subunit
authors W.Wong, X.C.Bai, A.Brown, I.S.Fernandez, E.Hanssen, M.Condron, Y.H J.Baum, S.H.W.Scheres
compound source
Molecule: 18s Ribosomal Rna
Chain: A
 Organism_scientific: Plasmodium Falciparum
Organism_taxid: 36329
Strain: 3d7

Molecule: 40s Ribosomal Protein Es1
Chain: B
Organism_scientific: Plasmodium Falciparum
Organism_taxid: 36329
Strain: 3d7

Molecule: 40s Ribosomal Protein Us2
Chain: C
Organism_scientific: Plasmodium Falciparum
Organism_taxid: 36329
Strain: 3d7

Molecule: 40s Ribosomal Protein Us3
Chain: D
Organism_scientific: Plasmodium Falciparum
Organism_taxid: 36329
Strain: 3d7

Molecule: 40s Ribosomal Protein Us4
Chain: E
Organism_scientific: Plasmodium Falciparum
Organism_taxid: 36329
Strain: 3d7

Molecule: 40s Ribosomal Protein Es4
Chain: F
Organism_scientific: Plasmodium Falciparum
Organism_taxid: 36329
Strain: 3d7

Molecule: 40s Ribosomal Protein Us5
Chain: G
Organism_scientific: Plasmodium Falciparum
Organism_taxid: 36329
Strain: 3d7

Molecule: 40s Ribosomal Protein Es6
Chain: H
Organism_scientific: Plasmodium Falciparum
Organism_taxid: 36329
Strain: 3d7

Molecule: 40s Ribosomal Protein Us7
Chain: I
Organism_scientific: Plasmodium Falciparum
Organism_taxid: 36329
Strain: 3d7

Molecule: 40s Ribosomal Protein Es7
Chain: J
Organism_scientific: Plasmodium Falciparum
Organism_taxid: 36329
Strain: 3d7

Molecule: 40s Ribosomal Protein Us8
Chain: K
Organism_scientific: Plasmodium Falciparum
Organism_taxid: 36329
Strain: 3d7

Molecule: 40s Ribosomal Protein Es8
Chain: L
Organism_scientific: Plasmodium Falciparum
Organism_taxid: 36329
Strain: 3d7

Molecule: 40s Ribosomal Protein Us9
Chain: M
Organism_scientific: Plasmodium Falciparum
Organism_taxid: 36329
Strain: 3d7

Molecule: 40s Ribosomal Protein Us10
Chain: N
Organism_scientific: Plasmodium Falciparum
Organism_taxid: 36329
Strain: 3d7

Molecule: 40s Ribosomal Protein Es10
Chain: O
Organism_scientific: Plasmodium Falciparum
Organism_taxid: 36329
Strain: 3d7

Molecule: 40s Ribosomal Protein Us11
Chain: P
Organism_scientific: Plasmodium Falciparum
Organism_taxid: 36329
Strain: 3d7

Molecule: 40s Ribosomal Protein Us12
Chain: Q
Organism_scientific: Plasmodium Falciparum
Organism_taxid: 36329
Strain: 3d7

Molecule: 40s Ribosomal Protein Es12
Chain: R
Organism_scientific: Plasmodium Falciparum
Organism_taxid: 36329
Strain: 3d7

Molecule: 40s Ribosomal Protein Us13
Chain: S
Organism_scientific: Plasmodium Falciparum
Organism_taxid: 36329
Strain: 3d7

Molecule: 40s Ribosomal Protein Us14
Chain: T
Organism_scientific: Plasmodium Falciparum
Organism_taxid: 36329
Strain: 3d7

Molecule: 40s Ribosomal Protein Us15
Chain: U
Organism_scientific: Plasmodium Falciparum
Organism_taxid: 36329
Strain: 3d7

Molecule: 40s Ribosomal Protein Us17
Chain: V
Organism_scientific: Plasmodium Falciparum
Organism_taxid: 36329
Strain: 3d7

Molecule: 40s Ribosomal Protein Es17
Chain: W
Organism_scientific: Plasmodium Falciparum
Organism_taxid: 36329
Strain: 3d7

Molecule: 40s Ribosomal Protein Us19
Chain: X
Organism_scientific: Plasmodium Falciparum
Organism_taxid: 36329
Strain: 3d7

Molecule: 40s Ribosomal Protein Es19
Chain: Y
Organism_scientific: Plasmodium Falciparum
Organism_taxid: 36329
Strain: 3d7

Molecule: 40s Ribosomal Protein Es21
Chain: Z
Organism_scientific: Plasmodium Falciparum
Organism_taxid: 36329
Strain: 3d7

Molecule: 40s Ribosomal Protein Es24
Chain: 1
Organism_scientific: Plasmodium Falciparum
Organism_taxid: 36329
Strain: 3d7

Molecule: 40s Ribosomal Protein Es25
Chain: 2
Organism_scientific: Plasmodium Falciparum
Organism_taxid: 36329
Strain: 3d7

Molecule: 40s Ribosomal Protein Es26
Chain: 3
Organism_scientific: Plasmodium Falciparum
Organism_taxid: 36329
Strain: 3d7

Molecule: 40s Ribosomal Protein Es27
Chain: 4
Organism_scientific: Plasmodium Falciparum
Organism_taxid: 36329
Strain: 3d7

Molecule: 40s Ribosomal Protein Es28
Chain: 5
Organism_scientific: Plasmodium Falciparum
Organism_taxid: 36329
Strain: 3d7

Molecule: 40s Ribosomal Protein Es30
Chain: 6
Organism_scientific: Plasmodium Falciparum
Organism_taxid: 36329
Strain: 3d7

Molecule: Trna
Chain: 7
Organism_scientific: Plasmodium Falciparum
Organism_taxid: 36329
Strain: 3d7
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 3.20 Å
ligand 34G, MG, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
1


2


3


4


5


6


B


C


D


E


F


G


H


I


J


K


L


M


N


O


P


Q


R


S


T


U


V


W


X


Y


Z


Primary referenceCryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine., Wong W, Bai XC, Brown A, Fernandez IS, Hanssen E, Condron M, Tan YH, Baum J, Scheres SH, Elife. 2014 Jun 9:e03080. doi: 10.7554/eLife.03080. PMID:24913268
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1402 Kb) [Save to disk]
  • Biological Unit Coordinates (3j7a.pdb1.gz) 1387 Kb
  • LPC: Ligand-Protein Contacts for 3J7A
  • CSU: Contacts of Structural Units for 3J7A
  • Retrieve 3J7A in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3J7A from S2C, [Save to disk]
    • View 3J7A in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 3J7A
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3J7A, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3j7a_L] [3j7a_4] [3j7a_S] [3j7a_U] [3j7a_O] [3j7a_7] [3j7a_P] [3j7a_V] [3j7a_E] [3j7a_I] [3j7a_N] [3j7a_K] [3j7a_M] [3j7a_C] [3j7a] [3j7a_Q] [3j7a_6] [3j7a_H] [3j7a_F] [3j7a_Y] [3j7a_G] [3j7a_Z] [3j7a_R] [3j7a_W] [3j7a_1] [3j7a_A] [3j7a_X] [3j7a_3] [3j7a_B] [3j7a_2] [3j7a_T] [3j7a_5] [3j7a_J] [3j7a_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3J7A: [KH] [KOW] [Ribosomal_S10] [Ribosomal_S13_N] [Ribosomal_S15] [Ribosomal_S19e] [Ribosomal_S3Ae] [Ribosomal_S4] [Ribosomal_S6e] [S4 ] by SMART
    • Other resources with information on 3J7A
  • Community annotation for 3J7A at PDBWiki (http://pdbwiki.org)

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science