6T7O

X-ray structure of the C-terminal domain of S. aureus Hibernating Promoting Factor (CTD-SaHPF)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 

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This is version 1.2 of the entry. See complete history


Literature

Dimerization of long hibernation promoting factor from Staphylococcus aureus: Structural analysis and biochemical characterization.

Usachev, K.S.Fatkhullin, B.F.Klochkova, E.A.Miftakhov, A.K.Golubev, A.A.Bikmullin, A.G.Nurullina, L.I.Garaeva, N.S.Islamov, D.R.Gabdulkhakov, A.G.Lekontseva, N.V.Tishchenko, S.V.Balobanov, V.A.Khusainov, I.S.Yusupov, M.M.Validov, S.Z.

(2020) J Struct Biol 209: 107408-107408

  • DOI: https://doi.org/10.1016/j.jsb.2019.107408
  • Primary Citation of Related Structures:  
    6T7O

  • PubMed Abstract: 

    Staphylococcus aureus hibernation promoting factor (SaHPF) is responsible for the formation of 100S ribosome dimers, which in turn help this pathogen to reduce energy spent under unfavorable conditions. Ribosome dimer formation strongly depends on the dimerization of the C-terminal domain of SaHPF (CTD SaHPF ). In this study, we solved the crystal structure of CTD SaHPF at 1.6 Å resolution and obtained a precise arrangement of the dimer interface. Residues Phe 160 , Val 162 , Thr 171 , Ile 173 , Tyr 175 , Ile 185 andThr 187 in the dimer interface of SaHPF protein were mutated and the effects were analyzed for the formation of 100S disomes of ribosomes isolated from S. aureus. It was shown that substitution of any of single residues Phe 160 , Val 162 , Ile 173 , Tyr 175 and Ile 185 in the SaHPF homodimer interface abolished the ribosome dimerization in vitro.


  • Organizational Affiliation

    Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya, Kazan 420008, Russian Federation.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome hibernation promotion factor
A, B
67Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: hpfSAOUHSC_00767
UniProt
Find proteins for Q2G055 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2G055 
Go to UniProtKB:  Q2G055
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2G055
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.855α = 90
b = 45.855β = 90
c = 117.644γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Science FoundationRussian Federation16 - 14 - 10014

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-11
    Type: Initial release
  • Version 1.1: 2020-01-22
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description