1T1M

Binding position of ribosome recycling factor (RRF) on the E. coli 70S ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 12 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Visualization of ribosome-recycling factor on the Escherichia coli 70S ribosome: Functional implications

Agrawal, R.K.Sharma, M.R.Kiel, M.C.Hirokawa, G.Booth, T.M.Spahn, C.M.Grassucci, R.A.Kaji, A.Frank, J.

(2004) Proc.Natl.Acad.Sci.USA 101: 8900-8905

  • DOI: 10.1073/pnas.0401904101
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • After the termination step of protein synthesis, a deacylated tRNA and mRNA remain associated with the ribosome. The ribosome-recycling factor (RRF), together with elongation factor G (EF-G), disassembles this posttermination complex into mRNA, tRNA, ...

    After the termination step of protein synthesis, a deacylated tRNA and mRNA remain associated with the ribosome. The ribosome-recycling factor (RRF), together with elongation factor G (EF-G), disassembles this posttermination complex into mRNA, tRNA, and the ribosome. We have obtained a three-dimensional cryo-electron microscopic map of a complex of the Escherichia coli 70S ribosome and RRF. We find that RRF interacts mainly with the segments of the large ribosomal subunit's (50S) rRNA helices that are involved in the formation of two central intersubunit bridges, B2a and B3. The binding of RRF induces considerable conformational changes in some of the functional domains of the ribosome. As compared to its binding position derived previously by hydroxyl radical probing study, we find that RRF binds further inside the intersubunit space of the ribosome such that the tip of its domain I is shifted (by approximately 13 A) toward protein L5 within the central protuberance of the 50S subunit, and domain II is oriented more toward the small ribosomal subunit (30S). Overlapping binding sites of RRF, EF-G, and the P-site tRNA suggest that the binding of EF-G would trigger the removal of deacylated tRNA from the P site by moving RRF toward the ribosomal E site, and subsequent removal of mRNA may be induced by a shift in the position of 16S rRNA helix 44, which harbors part of the mRNA.


    Related Citations: 
    • Structure of the 30S ribosomal subunit
      Wimberly, B.T.,Brodersen, D.E.,Clemons Jr., W.M.,Morgan-Warren, R.J.,Carter, A.P.,Vonrhein, C.,Hartsch, T.,Ramakrishnan, V.
      (2000) Nature 407: 327
    • High resolution structure of the large ribosomal subunit from a mesophilic eubacterium
      Harms, J.,Schluenzen, F.,Zarivach, R.,Bashan, A.,Gat, S.,Agmon, I.,Bartels, H.,Franceschi, F.,Yonath, A.
      (2001) Cell 107: 679
    • Crystal structure of Thermotoga maritima ribosome recycling factor: a tRNA mimic
      Selmer, M.,Al-Karadaghi, S.,Hirokawa, G.,Kaji, A.,Liljas, A.
      (1999) Science 286: 2349
    • Crystal structure of the ribosome recycling factor from Escherichia coli
      Kim, K.K.,Min, K.,Suh, S.W.
      (2000) Embo J. 19: 2362


    Organizational Affiliation

    Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509, USA. agrawal@wadsworth.org




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ribosome recycling factor
C
185Escherichia coliMutation(s): 0 
Gene Names: frr
Find proteins for P84154 (Escherichia coli)
Go to UniProtKB:  P84154
Entity ID: 1
MoleculeChainsLengthOrganism
dodecamer fragment of double helix from 23S rRNAA12Escherichia coli
Entity ID: 2
MoleculeChainsLengthOrganism
42-mer fragment of double helix from 16S rRNAB42Escherichia coli
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 12 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-06-15
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance