5NKO

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


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 500 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures and dynamics of hibernating ribosomes from Staphylococcus aureus mediated by intermolecular interactions of HPF.

Khusainov, I.Vicens, Q.Ayupov, R.Usachev, K.Myasnikov, A.Simonetti, A.Validov, S.Kieffer, B.Yusupova, G.Yusupov, M.Hashem, Y.

(2017) EMBO J. 36: 2073-2087

  • DOI: 10.15252/embj.201696105
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In bacteria, ribosomal hibernation shuts down translation as a response to stress, through reversible binding of stress-induced proteins to ribosomes. This process typically involves the formation of 100S ribosome dimers. Here, we present the structu ...

    In bacteria, ribosomal hibernation shuts down translation as a response to stress, through reversible binding of stress-induced proteins to ribosomes. This process typically involves the formation of 100S ribosome dimers. Here, we present the structures of hibernating ribosomes from human pathogen Staphylococcus aureus containing a long variant of the hibernation-promoting factor (SaHPF) that we solved using cryo-electron microscopy. Our reconstructions reveal that the N-terminal domain (NTD) of SaHPF binds to the 30S subunit as observed for shorter variants of HPF in other species. The C-terminal domain (CTD) of SaHPF protrudes out of each ribosome in order to mediate dimerization. Using NMR, we characterized the interactions at the CTD-dimer interface. Secondary interactions are provided by helix 26 of the 16S ribosomal RNA We also show that ribosomes in the 100S particle adopt both rotated and unrotated conformations. Overall, our work illustrates a specific mode of ribosome dimerization by long HPF, a finding that may help improve the selectivity of antimicrobials.


    Organizational Affiliation

    Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia.,Département de Biologie et de Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR7104, INSERM U964, Université de Strasbourg, Illkirch, France.,CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Université de Strasbourg, Strasbourg, France.,CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Université de Strasbourg, Strasbourg, France marat@igbmc.fr y.hashem@ibmc-cnrs.unistra.fr.,Département de Biologie et de Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR7104, INSERM U964, Université de Strasbourg, Illkirch, France marat@igbmc.fr y.hashem@ibmc-cnrs.unistra.fr.,Institute of Physics, Kazan Federal University, Kazan, Russia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribosome hibernation promotion factor
A, B
61Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: hpf
Find proteins for Q2G055 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2G055
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 500 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Science FoundationRussian Federation16-14-10014

Revision History 

  • Version 1.0: 2017-07-05
    Type: Initial release
  • Version 1.1: 2017-07-26
    Type: Database references
  • Version 1.2: 2019-05-08
    Type: Data collection