5T7V

Methicillin Resistant, Linezolid resistant Staphylococcus aureus 70S ribosome (delta S145 uL3)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural Basis for Linezolid Binding Site Rearrangement in theStaphylococcus aureusRibosome.

Belousoff, M.J.Eyal, Z.Radjainia, M.Ahmed, T.Bamert, R.S.Matzov, D.Bashan, A.Zimmerman, E.Mishra, S.Cameron, D.Elmlund, H.Peleg, A.Y.Bhushan, S.Lithgow, T.Yonath, A.

(2017) mBio 8

  • DOI: https://doi.org/10.1128/mBio.00395-17
  • Primary Citation of Related Structures:  
    5T7V, 5TCU

  • PubMed Abstract: 

    An unorthodox, surprising mechanism of resistance to the antibiotic linezolid was revealed by cryo-electron microscopy (cryo-EM) in the 70S ribosomes from a clinical isolate of Staphylococcus aureus This high-resolution structural information demonstrated that a single amino acid deletion in ribosomal protein uL3 confers linezolid resistance despite being located 24 Å away from the linezolid binding pocket in the peptidyl-transferase center. The mutation induces a cascade of allosteric structural rearrangements of the rRNA that ultimately results in the alteration of the antibiotic binding site. IMPORTANCE The growing burden on human health caused by various antibiotic resistance mutations now includes prevalent Staphylococcus aureus resistance to last-line antimicrobial drugs such as linezolid and daptomycin. Structure-informed drug modification represents a frontier with respect to designing advanced clinical therapies, but success in this strategy requires rapid, facile means to shed light on the structural basis for drug resistance (D. Brown, Nat Rev Drug Discov 14:821-832, 2015, https://doi.org/10.1038/nrd4675). Here, detailed structural information demonstrates that a common mechanism is at play in linezolid resistance and provides a step toward the redesign of oxazolidinone antibiotics, a strategy that could thwart known mechanisms of linezolid resistance.


  • Organizational Affiliation

    Infection & Immunity Program, Biomedicine Discovery Institute & Department of Microbiology, Monash University, Clayton, Australia.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10B [auth S1]82Staphylococcus aureusMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11C [auth S2]115Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12D [auth S3]136Staphylococcus aureusMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15E [auth S6]87Staphylococcus aureusMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16F [auth S7]76Staphylococcus aureusMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17G [auth S8]82Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18H [auth S9]55Staphylococcus aureusMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20I [auth SA]76Staphylococcus aureusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4J [auth SC]198Staphylococcus aureusMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5K [auth SD]154Staphylococcus aureusMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6L [auth SE]92Staphylococcus aureusMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8M [auth SF]130Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19P [auth L1]113Staphylococcus aureusMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2Q [auth L2]275Staphylococcus aureusMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20R [auth L3]116Staphylococcus aureusMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21S [auth L4]100Staphylococcus aureusMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22T [auth L5]111Staphylococcus aureusMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23U [auth L6]87Staphylococcus aureusMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24V [auth L7]101Staphylococcus aureusMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25W [auth L8]93Staphylococcus aureusMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27X [auth L9]78Staphylococcus aureusMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28Y [auth LA]59Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for A0A077URJ8 (Staphylococcus schweitzeri)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29Z [auth LB]61Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3AA [auth LC]214Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for W8U3W0 (Staphylococcus schweitzeri)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30BA [auth LD]57Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for W8UVN7 (Staphylococcus aureus)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32CA [auth LE]53Staphylococcus aureusMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33DA [auth LF]47Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for A0A077UXT4 (Staphylococcus schweitzeri)
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34EA [auth LG]44Staphylococcus aureusMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35FA [auth LH]64Staphylococcus aureusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36GA [auth LI]37Staphylococcus aureusMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4HA [auth LJ]204Staphylococcus aureusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6IA [auth LL]174Staphylococcus aureusMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13JA [auth LM]143Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14KA [auth LN]121Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for A0A077UUA0 (Staphylococcus schweitzeri)
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15LA [auth LO]144Staphylococcus aureusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16MA [auth LP]136Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17NA [auth LQ]121Staphylococcus aureusMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18OA [auth LR]116Staphylococcus aureusMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S ribosomal RNA1,547Staphylococcus aureus
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Entity ID: 14
MoleculeChains LengthOrganismImage
23S ribosomal RNAN [auth B]2,919Staphylococcus aureus
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Entity ID: 15
MoleculeChains LengthOrganismImage
5S ribosomal RNAO [auth C]114Staphylococcus aureus
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Entity ID: 42
MoleculeChains LengthOrganismImage
E-site tRNAPA [auth D]74Staphylococcus aureus
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth B]
BB [auth B]
CB [auth B]
DB [auth B]
EB [auth B]
AB [auth B],
BB [auth B],
CB [auth B],
DB [auth B],
EB [auth B],
FB [auth B],
GB [auth B],
QA [auth A],
RA [auth A],
SA [auth A],
TA [auth A],
UA [auth B],
VA [auth B],
WA [auth B],
XA [auth B],
YA [auth B],
ZA [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
NHMRCAustralia1092262

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-31
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Data collection, Experimental preparation
  • Version 1.2: 2018-02-21
    Changes: Database references
  • Version 1.3: 2018-03-28
    Changes: Data collection, Database references
  • Version 1.4: 2019-12-11
    Changes: Other