1Y69 Ribosome date Dec 04, 2004
title Rrf Domain I In Complex With The 50s Ribosomal Subunit From Deinococcus Radiodurans
authors D.N.Wilson, F.Schluenzen, J.M.Harms, T.Yoshida, T.Ohkubo, R.Albre J.Buerger, Y.Kobayashi, P.Fucini
compound source
Molecule: 23s Ribosomal Rna
Chain
Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230

Molecule: 5s Ribosomal Rna
Chain: 9

Organism_scientific: Deinococcus Radiodurans R1
Organism_taxid: 243230

Molecule: 50s Ribosomal Protein L16
Chain: K

Organism_scientific: Deinococcus Radiodurans (Strain Atcc 1 Dsm 20539 Jcm 16871 Lmg 4051 Nbrc 15346 Ncimb 9279 Vkm B-1422);
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: 50s Ribosomal Protein L27
Chain: U

Organism_scientific: Deinococcus Radiodurans (Strain Atcc 1 Dsm 20539 Jcm 16871 Lmg 4051 Nbrc 15346 Ncimb 9279 Vkm B-1422);
Organism_taxid: 243230
Strain: Atcc 13939 Dsm 20539 Jcm 16871 Lmg 4051 Nbr Ncimb 9279 R1 Vkm B-1422;

Molecule: Ribosome-Recycling Factor
Chain: 8
Fragment: Unp Residues 1-30 And 106-185
Synonym: Rrf,Ribosome-Releasing Factor
Engineered: Yes
Mutation: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K12
Gene: Frr, Rrf, B0172, Jw0167
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: I 2 2 2
R_factor 0.275 R_Free 0.338
crystal
cell
length a length b length c angle alpha angle beta angle gamma
168.700 405.000 693.000 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.33 Å
Gene
Ontology
ChainFunctionProcessComponent
8


K


U


Primary referenceX-ray crystallography study on ribosome recycling: the mechanism of binding and action of RRF on the 50S ribosomal subunit., Wilson DN, Schluenzen F, Harms JM, Yoshida T, Ohkubo T, Albrecht R, Buerger J, Kobayashi Y, Fucini P, EMBO J 2005 Jan 26;24(2):251-60. Epub 2004 Dec 23. PMID:15616575
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1114 Kb) [Save to disk]
  • Biological Unit Coordinates (1y69.pdb1.gz) 1108 Kb
  • CSU: Contacts of Structural Units for 1Y69
  • Likely Quarternary Molecular Structure file(s) for 1Y69
  • Structure Factors (1967 Kb)
  • Retrieve 1Y69 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1Y69 from S2C, [Save to disk]
  • View 1Y69 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 1Y69
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1Y69, from MSDmotif at EBI
  • Fold representative 1y69 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1y69_0] [1y69_9] [1y69_K] [1y69] [1y69_8] [1y69_U]
  • SWISS-PROT database: [Q9RXJ5] [Q9RY65] [P0A807]
  • Domain organization of [RL16_DEIRA] [RL27_DEIRA] [RRF_ECO57] by SWISSPFAM
  • Other resources with information on 1Y69
  • Community annotation for 1Y69 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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