6WRS

Structure of the 50S subunit of the ribosome from Methicillin Resistant Staphylococcus aureus in complex with the antibiotic, tedizolid

  • Classification: RIBOSOME
  • Organism(s): Staphylococcus aureus
  • Mutation(s): Yes 

  • Deposited: 2020-04-30 Released: 2020-06-03 
  • Deposition Author(s): Belousoff, M.J.
  • Funding Organization(s): Department of Defense (DOD, United States)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Characterization of the Core Ribosomal Binding Region for the Oxazolidone Family of Antibiotics Using Cryo-EM.

Wright, A.Deane-Alder, K.Marschall, E.Bamert, R.Venugopal, H.Lithgow, T.Lupton, D.W.Belousoff, M.J.

(2020) Acs Pharmacol Transl Sci 3: 425-432

  • DOI: 10.1021/acsptsci.0c00041
  • Primary Citation of Related Structures:  
    6WQQ, 6WRS, 6WRU, 6WQN

  • PubMed Abstract: 
  • Linezolid and tedizolid are oxazolidinones with established clinical utility for the treatment of Gram-positive pathogens. Over time it has become apparent that even modest structural changes to the core phenyl oxazolidinone leads to drastic changes in biological activity ...

    Linezolid and tedizolid are oxazolidinones with established clinical utility for the treatment of Gram-positive pathogens. Over time it has become apparent that even modest structural changes to the core phenyl oxazolidinone leads to drastic changes in biological activity. Consequently, the structure-activity relationship around the core oxazolidinone is constantly evolving, often reflected with new structural motifs present in nascent oxazolidinones. Herein we describe the use of cryo-electron microscopy to examine the differences in binding of several functionally different oxazolidinones in the hopes of enhanced understanding of their SAR. Tedizolid, radezolid, T145, and contezolid have been examined within the peptidyl transferase center (PTC) of the 50S ribosomal subunit from methicillin resistant Staphylococcus aureus . The ribosome-antibiotic complexes were resolved to a resolution of around 3 Å enabling unambiguous assignment of how each antibiotic interacts with the PTC.


    Organizational Affiliation

    Drug and Development Biology, Monash Institute of Pharmaceutical Sciences, Monash University, 399 Royal Parade, Parkville, 3052 Victoria, Australia.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19A116Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for Q2FZ42 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2B277Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for P60430 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20C118Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for Q2FXQ1 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21D105Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
uL22E117Staphylococcus aureusMutation(s): 1 
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23F91Staphylococcus aureusMutation(s): 1 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24G105Staphylococcus aureusMutation(s): 1 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
uL25H107Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 9
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50S ribosomal protein L28I [auth J]62Staphylococcus aureusMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29J [auth K]72Staphylococcus aureusMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3K [auth L]217Staphylococcus aureusMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30L [auth M]58Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 13
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50S ribosomal protein L32M [auth N]57Staphylococcus aureusMutation(s): 1 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33N [auth O]49Staphylococcus aureusMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34O [auth P]50Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35P [auth Q]65Staphylococcus aureusMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36Q [auth R]37Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4R [auth S]207Staphylococcus aureusMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13S [auth V]145Staphylococcus aureusMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14T [auth W]122Staphylococcus aureusMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15U [auth X]146Staphylococcus aureusMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16V [auth Y]144Staphylococcus aureusMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17W [auth Z]122Staphylococcus aureusMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18X [auth a]119Staphylococcus aureusMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27AA [auth I]85Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for Q2FXT0 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 25
MoleculeChainsLengthOrganismImage
23S rRNAY [auth 1]2923Staphylococcus aureus
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Entity ID: 26
MoleculeChainsLengthOrganismImage
5S rRNAZ [auth 2]115Staphylococcus aureus
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
U7V (Subject of Investigation/LOI)
Query on U7V

Download Ideal Coordinates CCD File 
BA [auth 1]Tedizolid
C17 H15 F N6 O3
XFALPSLJIHVRKE-GFCCVEGCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2020-04-30 
  • Released Date: 2020-06-03 
  • Deposition Author(s): Belousoff, M.J.

Funding OrganizationLocationGrant Number
Department of Defense (DOD, United States)United StatesW81XWH1910126

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-03
    Type: Initial release
  • Version 1.1: 2020-12-16
    Changes: Database references