Biological Assembly 1  

 3D View: Structure | Electron Density

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - ABC 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 1011896.56 
• Atom Count: 64484 
• Residue Count: 3349 
• Unique protein chains: 3
• Unique nucleic acid chains: 2

1Y69

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

• DOI: 10.2210/pdb1Y69/pdb
• NDB: RR0099

• Classification: RIBOSOME
• Organism(s): Deinococcus radiodurans R1, Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422), Escherichia coli (strain K12)
• Expression System: Escherichia coli


• Deposited: 2004-12-04 Released: 2005-03-01 
• Deposition Author(s): Wilson, D.N., Schluenzen, F., Harms, J.M., Yoshida, T., Ohkubo, T., Albrecht, R., Buerger, J., Kobayashi, Y., Fucini, P.

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Experimental Data Snapshot

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

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

• PubMed: 15616575 
• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L16	K	141	Deinococcus 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
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L27	U	91	Deinococcus 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
Molecule	Chains	Sequence Length	Organism	Details
Ribosome-recycling factor	8	113	Escherichia 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
Molecule	Chains	Length	Organism
23S ribosomal RNA	0	2880	Deinococcus radiodurans R1

Entity ID: 2
Molecule	Chains	Length	Organism
5S ribosomal RNA	9	124	Deinococcus 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 = 168.700	α = 90.00
b = 405.000	β = 90.00
c = 693.000	γ = 90.00

Software Package:

Software Name	Purpose
CNS	phasing
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-12-04 
• Released Date: 2005-03-01 
• Deposition Author(s): Wilson, D.N., Schluenzen, F., Harms, J.M., Yoshida, T., Ohkubo, T., Albrecht, R., Buerger, J., Kobayashi, Y., Fucini, P.

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