6SJ6

Cryo-EM structure of 50S-RsfS complex from Staphylococcus aureus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.23 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Mechanism of ribosome shutdown by RsfS in Staphylococcus aureus revealed by integrative structural biology approach.

Khusainov, I.Fatkhullin, B.Pellegrino, S.Bikmullin, A.Liu, W.T.Gabdulkhakov, A.Shebel, A.A.Golubev, A.Zeyer, D.Trachtmann, N.Sprenger, G.A.Validov, S.Usachev, K.Yusupova, G.Yusupov, M.

(2020) Nat Commun 11: 1656-1656

  • DOI: https://doi.org/10.1038/s41467-020-15517-0
  • Primary Citation of Related Structures:  
    6SJ5, 6SJ6

  • PubMed Abstract: 

    For the sake of energy preservation, bacteria, upon transition to stationary phase, tone down their protein synthesis. This process is favored by the reversible binding of small stress-induced proteins to the ribosome to prevent unnecessary translation. One example is the conserved bacterial ribosome silencing factor (RsfS) that binds to uL14 protein onto the large ribosomal subunit and prevents its association with the small subunit. Here we describe the binding mode of Staphylococcus aureus RsfS to the large ribosomal subunit and present a 3.2 Å resolution cryo-EM reconstruction of the 50S-RsfS complex together with the crystal structure of uL14-RsfS complex solved at 2.3 Å resolution. The understanding of the detailed landscape of RsfS-uL14 interactions within the ribosome shed light on the mechanism of ribosome shutdown in the human pathogen S. aureus and might deliver a novel target for pharmacological drug development and treatment of bacterial infections.


  • Organizational Affiliation

    Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kremlyovskaya Street 18, Kazan, 420008, Russia. iskander.khusainov@biophys.mpg.de.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2C [auth D]277Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for P60430 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Go to UniProtKB:  P60430
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3D [auth E]220Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FW06 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Go to UniProtKB:  Q2FW06
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4E [auth F]207Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FW07 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Go to UniProtKB:  Q2FW07
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13F [auth M]145Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FW38 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Go to UniProtKB:  Q2FW38
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14G [auth N]122Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FW16 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Go to UniProtKB:  Q2FW16
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15H [auth O]146Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for P0A0F8 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Go to UniProtKB:  P0A0F8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16I [auth P]144Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FW13 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Go to UniProtKB:  Q2FW13
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17J [auth Q]122Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FW33 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Go to UniProtKB:  Q2FW33
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18K [auth R]119Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FW22 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Go to UniProtKB:  Q2FW22
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19L [auth S]116Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FZ42 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Go to UniProtKB:  Q2FZ42
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20M [auth T]118Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FXQ1 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Go to UniProtKB:  Q2FXQ1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21N [auth U]102Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FXS8 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Go to UniProtKB:  Q2FXS8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22O [auth V]117Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FW11 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Go to UniProtKB:  Q2FW11
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23P [auth W]91Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FW08 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Go to UniProtKB:  Q2FW08
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24Q [auth X]105Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FW17 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Go to UniProtKB:  Q2FW17
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25R [auth Y]217Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2G0S0 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Go to UniProtKB:  Q2G0S0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27S [auth Z]94Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FXT0 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Go to UniProtKB:  Q2FXT0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28T [auth 0]62Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FZ60 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Go to UniProtKB:  Q2FZ60
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29U [auth 1]69Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FW14 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Go to UniProtKB:  Q2FW14
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30V [auth 2]59Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for P0A0G2 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Go to UniProtKB:  P0A0G2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32W [auth 4]58Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FZF1 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Go to UniProtKB:  Q2FZF1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34X [auth 6]45Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FUQ0 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Go to UniProtKB:  Q2FUQ0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35Y [auth 7]66Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FXQ0 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Go to UniProtKB:  Q2FXQ0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal silencing factor RsfSZ [auth 9]117Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rsfSSAOUHSC_01695
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
23S ribosomal RNA2,923Staphylococcus aureus subsp. aureus NCTC 8325
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
5S ribosomal RNA115Staphylococcus aureus subsp. aureus NCTC 8325
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download Ideal Coordinates CCD File 
EC [auth A],
FC [auth A],
GC [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth A]
AC [auth A]
BA [auth A]
BB [auth A]
AA [auth A],
AB [auth A],
AC [auth A],
BA [auth A],
BB [auth A],
BC [auth A],
CA [auth A],
CB [auth A],
CC [auth A],
DA [auth A],
DB [auth A],
DC [auth A],
EA [auth A],
EB [auth A],
FA [auth A],
FB [auth A],
GA [auth A],
GB [auth A],
HA [auth A],
HB [auth A],
IA [auth A],
IB [auth A],
JA [auth A],
JB [auth A],
KA [auth A],
KB [auth A],
LA [auth A],
LB [auth A],
MA [auth A],
MB [auth A],
NA [auth A],
NB [auth A],
OA [auth A],
OB [auth A],
PA [auth A],
PB [auth A],
QA [auth A],
QB [auth A],
RA [auth A],
RB [auth A],
SA [auth A],
SB [auth A],
TA [auth A],
TB [auth A],
UA [auth A],
UB [auth A],
VA [auth A],
VB [auth A],
WA [auth A],
WB [auth A],
XA [auth A],
XB [auth A],
YA [auth A],
YB [auth A],
ZA [auth A],
ZB [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.23 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.1
MODEL REFINEMENTPHENIX
MODEL REFINEMENTCoot
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-15-CE11-0021-01
French National Research AgencyFranceANR-16-CE11-0007-01
French National Research AgencyFranceLabex: ANR-10-LABX- 0036_NETRNA

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-08
    Type: Initial release
  • Version 1.1: 2020-04-15
    Changes: Database references
  • Version 1.2: 2020-07-08
    Changes: Structure summary
  • Version 1.3: 2024-05-22
    Changes: Data collection, Database references, Derived calculations, Refinement description