1Y69

RRF domain I in complex with the 50S ribosomal subunit from Deinococcus radiodurans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.33 Å
  • R-Value Free: 0.338 
  • R-Value Work: 0.275 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

X-ray crystallography on ribosome recycling: mechanism of binding and action of RRF on the 50S ribosomal subunit

Wilson, D.N.Schluenzen, F.Harms, J.M.Yoshida, T.Ohkubo, T.Albrecht, R.Buerger, J.Kobayashi, Y.Fucini, P.

(2005) EMBO J. 24: 251-260

  • DOI: 10.1038/sj.emboj.7600525

  • PubMed Abstract: 
  • This study presents the crystal structure of domain I of the Escherichia coli ribosome recycling factor (RRF) bound to the Deinococcus radiodurans 50S subunit. The orientation of RRF is consistent with the position determined on a 70S-RRF complex by ...

    This study presents the crystal structure of domain I of the Escherichia coli ribosome recycling factor (RRF) bound to the Deinococcus radiodurans 50S subunit. The orientation of RRF is consistent with the position determined on a 70S-RRF complex by cryoelectron microscopy (cryo-EM). Alignment, however, requires a rotation of 7 degrees and a shift of the cryo-EM RRF by a complete turn of an alpha-helix, redefining the contacts established with ribosomal components. At 3.3 A resolution, RRF is seen to interact exclusively with ribosomal elements associated with tRNA binding and/or translocation. Furthermore, these results now provide a high-resolution structural description of the conformational changes that were suspected to occur on the 70S-RRF complex, which has implications for the synergistic action of RRF with elongation factor G (EF-G). Specifically, the tip of the universal bridge element H69 is shifted by 20 A toward h44 of the 30S subunit, suggesting that RRF primes the intersubunit bridge B2a for the action of EF-G. Collectively, our data enable a model to be proposed for the dual action of EF-G and RRF during ribosome recycling.


    Organizational Affiliation

    Max-Planck-Institute for Molecular Genetics, Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
K
141Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)Mutation(s): 0 
Gene Names: rplP
Find proteins for Q9RXJ5 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
Go to UniProtKB:  Q9RXJ5
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
U
91Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)Mutation(s): 0 
Gene Names: rpmA
Find proteins for Q9RY65 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
Go to UniProtKB:  Q9RY65
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Ribosome-recycling factor
8
113Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: frr (rrf)
Find proteins for P0A805 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A805
Entity ID: 1
MoleculeChainsLengthOrganism
23S ribosomal RNA02880Deinococcus radiodurans R1
Entity ID: 2
MoleculeChainsLengthOrganism
5S ribosomal RNA9124Deinococcus radiodurans R1
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.33 Å
  • R-Value Free: 0.338 
  • R-Value Work: 0.275 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 168.700α = 90.00
b = 405.000β = 90.00
c = 693.000γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-03-01
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-06-28
    Type: Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 1.4: 2017-08-02
    Type: Structure summary