6SJ6 image
Deposition Date 2019-08-12
Release Date 2020-04-08
Last Version Date 2024-05-22
Entry Detail
PDB ID:
6SJ6
Keywords:
Title:
Cryo-EM structure of 50S-RsfS complex from Staphylococcus aureus
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
3.23 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:T (auth: 0)
Chain Length:62
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:U (auth: 1)
Chain Length:69
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:V (auth: 2)
Chain Length:59
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:W (auth: 4)
Chain Length:58
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:X (auth: 6)
Chain Length:45
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:Y (auth: 7)
Chain Length:66
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:Ribosomal silencing factor RsfS
Gene (Uniprot):rsfS
Chain IDs:Z (auth: 9)
Chain Length:117
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:A
Chain Length:2923
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:B
Chain Length:115
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:C (auth: D)
Chain Length:277
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:D (auth: E)
Chain Length:220
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:E (auth: F)
Chain Length:207
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:F (auth: M)
Chain Length:145
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:G (auth: N)
Chain Length:122
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:H (auth: O)
Chain Length:146
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:I (auth: P)
Chain Length:144
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:J (auth: Q)
Chain Length:122
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:K (auth: R)
Chain Length:119
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:L (auth: S)
Chain Length:116
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:M (auth: T)
Chain Length:118
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:N (auth: U)
Chain Length:102
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:O (auth: V)
Chain Length:117
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:P (auth: W)
Chain Length:91
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:Q (auth: X)
Chain Length:105
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:R (auth: Y)
Chain Length:217
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:S (auth: Z)
Chain Length:94
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
Primary Citation
Mechanism of ribosome shutdown by RsfS in Staphylococcus aureus revealed by integrative structural biology approach.
Nat Commun 11 1656 1656 (2020)
PMID: 32245971 DOI: 10.1038/s41467-020-15517-0

Abstact

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.

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