3VQT

Crystal structure analysis of the translation factor RF3

• PDB DOI: https://doi.org/10.2210/pdb3VQT/pdb

• Classification: TRANSLATION
• Organism(s): Nitratidesulfovibrio vulgaris str. 'Miyazaki F
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-03-30 Released: 2012-09-05 
• Deposition Author(s): Kihira, K., Shomura, Y., Shibata, N., Kitamura, M., Higuchi, Y.

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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 

Starting Model: experimental

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

• PubMed: 22975312 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 5 generated by PISA (software)

Biological Assembly 6  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 6 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 247.26 kDa 
• Atom Count: 16,607 
• Modelled Residue Count: 1,970 
• Deposited Residue Count: 2,192 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide chain release factor 3	A, B, C, D	548	Nitratidesulfovibrio vulgaris str. 'Miyazaki F	Mutation(s): 0  Gene Names: DvMF_2372, prfC
UniProt
Find proteins for B8DIL5 (Nitratidesulfovibrio vulgaris (strain DSM 19637 / Miyazaki F)) Explore B8DIL5  Go to UniProtKB:  B8DIL5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	E [auth A], F [auth B], G [auth C], H [auth D]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N

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 = 47.387	α = 104.21
b = 82.795	β = 89.78
c = 148.293	γ = 89.63

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-05 
Deposition Author(s): Kihira, K., Shomura, Y., Shibata, N., Kitamura, M., Higuchi, Y.

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
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description