3J0D Translation date Jun 29, 2011
title Models For The T. Thermophilus Ribosome Recycling Factor Bou E. Coli Post-Termination Complex
authors T.Yokoyama, T.R.Shaikh, N.Iwakura, H.Kaji, A.Kaji, R.K.Agrawal
compound source
Molecule: Ribosomal 23s Rna
Chain: A
Fragment: Helices 43 And 44
 Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: Ribosomal 23s Rna
Chain: B
Fragment: Helix 69
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: Ribosomal 23s Rna
Chain: C
Fragment: Helix 71
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: Ribosomal 23s Rna
Chain: D
Fragment: Helix 80
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: Ribosomal 23s Rna
Chain: E
Fragment: Helix 93
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: Ribosomal 23s Rna
Chain: F
Fragment: Helix 95
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L11
Chain: G
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: Ribosomal 16s Rna
Chain: H
Fragment: Helix 44 Strand 1
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: Ribosomal 16s Rna
Chain: h
Fragment: Helix 44 Strand 2
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 30s Ribosomal Protein S12
Chain: I
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: Ribosome-Recycling Factor
Chain: J
Synonym: Rrf, Ribosome-Releasing Factor
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274
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 11.10 Å
Gene
Ontology
ChainFunctionProcessComponent
G


I


J


Primary referenceStructural insights into initial and intermediate steps of the ribosome-recycling process., Yokoyama T, Shaikh TR, Iwakura N, Kaji H, Kaji A, Agrawal RK, EMBO J. 2012 Mar 2;31(7):1836-46. doi: 10.1038/emboj.2012.22. PMID:22388519
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (132 Kb) [Save to disk]
  • Biological Unit Coordinates (3j0d.pdb1.gz) 127 Kb
  • CSU: Contacts of Structural Units for 3J0D
  • Retrieve 3J0D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3J0D from S2C, [Save to disk]
    • View 3J0D 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 3J0D
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3J0D, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3j0d_J] [3j0d_D] [3j0d_h] [3j0d_G] [3j0d_A] [3j0d_B] [3j0d] [3j0d_H] [3j0d_I] [3j0d_E] [3j0d_C] [3j0d_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3J0D: [RL11 ] by SMART
    • Other resources with information on 3J0D
  • Community annotation for 3J0D at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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