7P48

Staphylococcus aureus ribosome in complex with Sal(B)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Sal-type ABC-F proteins: intrinsic and common mediators of pleuromutilin resistance by target protection in staphylococci.

Mohamad, M., Nicholson, D., Saha, C.K., Hauryliuk, V., Edwards, T.A., Atkinson, G.C., Ranson, N.A., O'Neill, A.J.

(2022) Nucleic Acids Res 50: 2128-2142

  • DOI: https://doi.org/10.1093/nar/gkac058
  • Primary Citation of Related Structures:  
    7P48

  • PubMed Abstract: 

    The first member of the pleuromutilin (PLM) class suitable for systemic antibacterial chemotherapy in humans recently entered clinical use, underscoring the need to better understand mechanisms of PLM resistance in disease-causing bacterial genera. Of the proteins reported to mediate PLM resistance in staphylococci, the least-well studied to date is Sal(A), a putative ABC-F NTPase that-by analogy to other proteins of this type-may act to protect the ribosome from PLMs. Here, we establish the importance of Sal proteins as a common source of PLM resistance across multiple species of staphylococci. Sal(A) is revealed as but one member of a larger group of Sal-type ABC-F proteins that vary considerably in their ability to mediate resistance to PLMs and other antibiotics. We find that specific sal genes are intrinsic to particular staphylococcal species, and show that this gene family is likely ancestral to the genus Staphylococcus. Finally, we solve the cryo-EM structure of a representative Sal-type protein (Sal(B)) in complex with the staphylococcal 70S ribosome, revealing that Sal-type proteins bind into the E site to mediate target protection, likely by displacing PLMs and other antibiotics via an allosteric mechanism.

    • Organizational Affiliation: 

    Astbury Centre for Structural Molecular Biology and School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33A [auth 1]49Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for A0A077V2P0 (Staphylococcus schweitzeri)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34B [auth 2]45Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for A0A0D1JMX2 (Staphylococcus aureus)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35C [auth 3]66Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for A0A077UL47 (Staphylococcus schweitzeri)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36D [auth 4]37Staphylococcus aureusMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ABC-F type ribosomal protection proteinF [auth 6]565Mammaliicoccus lentusMutation(s): 0 
Gene Names: abc-f, H3V22_03170
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2J [auth C]276Staphylococcus aureusMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3K [auth D]220Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4L [auth E]207Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5M [auth F]179Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6N [auth G]178Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13O [auth H]145Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14P [auth I]122Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15Q [auth J]146Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16R [auth K]144Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17S [auth L]122Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18T [auth M]119Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19U [auth N]116Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20V [auth O]118Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21W [auth P]102Staphylococcus aureusMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22X [auth Q]117Staphylococcus aureusMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23Y [auth R]91Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24Z [auth S]105Staphylococcus aureusMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25AA [auth T]219Staphylococcus aureusMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
LSU ribosomal protein L27PBA [auth U]94Staphylococcus aureusMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28CA [auth V]62Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29DA [auth W]69Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for A0A0D1IHY2 (Staphylococcus aureus)
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30EA [auth X]59Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31 type BFA [auth Y]125Staphylococcus aureusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32GA [auth Z]57Staphylococcus aureusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2IA [auth b]232Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for A0A2X2M020 (Staphylococcus aureus)
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3JA [auth c]217Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for A0A077UU26 (Staphylococcus schweitzeri)
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4KA [auth d]200Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5LA [auth e]166Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6MA [auth f]98Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7NA [auth g]156Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8OA [auth h]132Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9PA [auth i]130Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for A0A1Q4GY48 (Staphylococcus aureus)
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10QA [auth j]102Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11RA [auth k]129Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12SA [auth l]149Staphylococcus aureusMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13TA [auth m]121Staphylococcus aureusMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZUA [auth n]61Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15VA [auth o]89Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16WA [auth p]91Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17XA [auth q]87Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for A0A077VLD5 (Staphylococcus schweitzeri)
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18YA [auth r]80Staphylococcus aureusMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19ZA [auth s]108Staphylococcus aureusMutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20AB [auth t]83Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains LengthOrganismImage
P-site tRNAE [auth 5]73Staphylococcus aureus
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Entity ID: 7
MoleculeChains LengthOrganismImage
mRNAG [auth 7]3Staphylococcus aureus
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Entity ID: 8
MoleculeChains LengthOrganismImage
23S rRNAH [auth A]2,921Staphylococcus aureus
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Entity ID: 9
MoleculeChains LengthOrganismImage
5S rRNAI [auth B]115Staphylococcus aureus
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Entity ID: 34
MoleculeChains LengthOrganismImage
16S rRNAHA [auth a]1,548Staphylococcus aureus
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP
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CB [auth 6],
DB [auth 6]		ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ZN
Query on ZN
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BB [auth 4],
GB [auth Z],
HB [auth n]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
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EB [auth 6],
FB [auth 6]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom203743/Z/16/Z

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-02
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references
  • Version 1.2: 2022-03-09
    Changes: Database references