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 
  • R-Value Observed: 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
  • Primary Citation of Related Structures:  
    1Y69

  • 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 cryoelectron microscopy (cryo-EM) ...

    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

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16C [auth K]141Deinococcus radiodurans R1Mutation(s): 0 
Gene Names: rplP, DR_0318
UniProt
Find proteins for Q9RXJ5 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
Explore Q9RXJ5 
Go to UniProtKB:  Q9RXJ5
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UniProt GroupQ9RXJ5
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27D [auth U]91Deinococcus radiodurans R1Mutation(s): 0 
Gene Names: rpmA, DR_0085
UniProt
Find proteins for Q9RY65 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
Explore Q9RY65 
Go to UniProtKB:  Q9RY65
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UniProt GroupQ9RY65
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome-recycling factorE [auth 8]113Escherichia coli K-12Mutation(s): 0 
Gene Names: frr, rrf, b0172, JW0167
UniProt
Find proteins for P0A805 (Escherichia coli (strain K12))
Explore P0A805 
Go to UniProtKB:  P0A805
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UniProt GroupP0A805
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S ribosomal RNAA [auth 0]2880Deinococcus radiodurans R1
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S ribosomal RNAB [auth 9]124Deinococcus radiodurans R1
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.33 Å
  • R-Value Free: 0.338 
  • R-Value Work: 0.275 
  • R-Value Observed: 0.275 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.7α = 90
b = 405β = 90
c = 693γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

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