3VQT

Crystal structure analysis of the translation factor RF3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

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This is version 1.3 of the entry. See complete history


Literature

Crystal structure analysis of the translation factor RF3 (release factor 3)

Kihira, K.Shimizu, Y.Shomura, Y.Shibata, N.Kitamura, M.Nakagawa, A.Ueda, T.Ochi, K.Higuchi, Y.

(2012) FEBS Lett 586: 3705-3709

  • DOI: https://doi.org/10.1016/j.febslet.2012.08.029
  • Primary Citation of Related Structures:  
    3VQT, 3VR1

  • PubMed Abstract: 

    The bacterial translational GTPases release factor RF3 promotes translation termination by recycling RF1 or RF2. Here, we present the crystal structures of RF3 complexed with GDP and guanosine 3',5'-(bis)diphosphate (ppGpp) at resolutions of 1.8 and 3.0Å, respectively. ppGpp is involved in the so-called "stringent response" of bacteria. ppGpp binds at the same site as GDP, suggesting that GDP and ppGpp are two alternative physiologically relevant ligands of RF3. We also found that ppGpp decelerates the recycling of RF1 by RF3. These lines of evidence suggest that RF3 functions both as a cellular metabolic sensor and as a regulator.


  • Organizational Affiliation

    Graduate School of Life Science, University of Hyogo, Ako 678-1297, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide chain release factor 3
A, B, C, D
548Nitratidesulfovibrio vulgaris str. 'Miyazaki FMutation(s): 0 
Gene Names: DvMF_2372prfC
UniProt
Find proteins for B8DIL5 (Desulfovibrio vulgaris (strain DSM 19637 / Miyazaki F))
Explore B8DIL5 
Go to UniProtKB:  B8DIL5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8DIL5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.387α = 104.21
b = 82.795β = 89.78
c = 148.293γ = 89.63
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-05
    Type: Initial release
  • Version 1.1: 2013-07-31
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description