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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1016/j.febslet.2012.08.029
  • Structures With Same Primary Citation

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptide chain release factor 3
A, B, C, D
548Desulfovibrio vulgaris str. 'Miyazaki FMutation(s): 0 
Gene Names: DvMF_2372, prfC
Find proteins for B8DIL5 (Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637))
Go to UniProtKB:  B8DIL5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP
Download CCD File 
A, B, C, D
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N		 Ligand Interaction
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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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • 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