1EK8

CRYSTAL STRUCTURE OF THE RIBOSOME RECYCLING FACTOR (RRF) FROM ESCHERICHIA COLI

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.235 

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This is version 1.2 of the entry. See complete history. 


Literature

Crystal structure of the ribosome recycling factor from Escherichia coli.

Kim, K.K., Min, K., Suh, S.W.

(2000) EMBO J 19: 2362-2370

  • DOI: 10.1093/emboj/19.10.2362
  • Primary Citation of Related Structures:  
    1EK8

  • PubMed Abstract: 

    • We have determined the crystal structure of the Escherichia coli ribosome recycling factor (RRF), which catalyzes the disassembly of the termination complex in protein synthesis. The L-shaped molecule consists of two domains: a triple-stranded antiparallel coiled-coil and an alpha/beta domain ...

    We have determined the crystal structure of the Escherichia coli ribosome recycling factor (RRF), which catalyzes the disassembly of the termination complex in protein synthesis. The L-shaped molecule consists of two domains: a triple-stranded antiparallel coiled-coil and an alpha/beta domain. The coil domain has a cylindrical shape and negatively charged surface, which are reminiscent of the anticodon arm of tRNA and domain IV of elongation factor EF-G. We suggest that RRF binds to the ribosomal A-site through its coil domain, which is a tRNA mimic. The relative position of the two domains is changed about an axis along the hydrophobic cleft in the hinge where the alkyl chain of a detergent molecule is bound. The tRNA mimicry and the domain movement observed in RRF provide a structural basis for understanding the role of RRF in protein synthesis.

    Related Citations: 
    • Crystallization and Preliminary Crystallographic Studies of Ribosome Recycling Factor from Escherichia coli.
      Yun, J., Kim, W., Ha, S.C., Eom, S.H., Suh, S.W., Kim, K.K.
      (2000) Acta Crystallogr D Biol Crystallogr 56: 84
    Organizational Affiliation: 

    Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Chinju 660-701, Korea. kim@px1.gsnu.ac.kr



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOME RECYCLING FACTORA185Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A805 (Escherichia coli (strain K12))
Explore P0A805 
Go to UniProtKB:  P0A805
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A805
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HG
Query on HG
Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]		MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N		 Ligand Interaction
DEM
Query on DEM
Download Ideal Coordinates CCD File 
E [auth A]DECYLOXY-METHANOL
C11 H24 O2
CDMVCFBAVCCGIE-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.235 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.064α = 90
b = 48.064β = 90
c = 142.273γ = 120
Software Package:
Software NamePurpose
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-03-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance