3J16 Ribosome date Dec 12, 2011
title Models Of Ribosome-Bound Dom34p And Rli1p And Their Ribosoma Partners
authors T.Becker, S.Franckenberg, S.Wickles, C.J.Shoemaker, A.M.Anger, J. P.Armache, H.Sieber, C.Ungewickell, O.Berninghausen, I.Daberkow A.Karcher, M.Thomm, K.P.Hopfner, R.Green, R.Beckmann
compound source
Molecule: Dom34p
Chain: A
 Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932

Molecule: Rli1p
Chain: B
Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932

Molecule: 28s Ribosomal Rna
Chain: J
Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932

Molecule: 18s Ribosomal Rna
Chain: K
Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932

Molecule: P-Site Trna
Chain: L
Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932

Molecule: 60s Ribosomal Protein L6
Chain: F
Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932

Molecule: 40s Ribosomal Protein S30e
Chain: E
Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932

Molecule: 60s Ribosomal Protein L10
Chain: G
Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932

Molecule: 40s Ribosomal Protein S6e
Chain: C
Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932

Molecule: 60s Ribosomal Protein L11
Chain: H
Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932

Molecule: 40s Ribosomal Protein S24e
Chain: I
Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932

Molecule: 40s Ribosomal Protein S24-A
Chain: D
Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932
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 7.20 Å
ligand ATP, MG, SF4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A
  • nuclease activity
  • endonuclease activity
  • endoribonuclease activity


    • B


    C

  • cytosolic small ribosomal su...
    • D


    E


    F


    G


    H

  • cytosolic large ribosomal su...
    • I

  • cytosolic large ribosomal su...
    • Primary referenceStructural basis of highly conserved ribosome recycling in eukaryotes and archaea., Becker T, Franckenberg S, Wickles S, Shoemaker CJ, Anger AM, Armache JP, Sieber H, Ungewickell C, Berninghausen O, Daberkow I, Karcher A, Thomm M, Hopfner KP, Green R, Beckmann R, Nature. 2012 Feb 22;482(7386):501-6. doi: 10.1038/nature10829. PMID:22358840
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (447 Kb) [Save to disk]
  • Biological Unit Coordinates (3j16.pdb1.gz) 439 Kb
  • LPC: Ligand-Protein Contacts for 3J16
  • CSU: Contacts of Structural Units for 3J16
  • Retrieve 3J16 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3J16 from S2C, [Save to disk]
    • View 3J16 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 3J16
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3J16, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3j16_D] [3j16_E] [3j16_K] [3j16_C] [3j16_H] [3j16_A] [3j16_B] [3j16_J] [3j16_F] [3j16_G] [3j16_L] [3j16] [3j16_I]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3J16: [AAA] [RL11] [Ribosomal_L14] [Ribosomal_S6e] [eRF1_1 ] by SMART
    • Other resources with information on 3J16
  • Community annotation for 3J16 at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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