6S12

Erythromycin Resistant Staphylococcus aureus 50S ribosome (delta R88 A89 uL22).


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 1.0 of the entry. See complete history


Literature

Exit tunnel modulation as resistance mechanism of S. aureus erythromycin resistant mutant.

Halfon, Y.Matzov, D.Eyal, Z.Bashan, A.Zimmerman, E.Kjeldgaard, J.Ingmer, H.Yonath, A.

(2019) Sci Rep 9: 11460-11460

  • DOI: https://doi.org/10.1038/s41598-019-48019-1
  • Primary Citation of Related Structures:  
    6S0X, 6S0Z, 6S12, 6S13

  • PubMed Abstract: 

    The clinical use of the antibiotic erythromycin (ery) is hampered owing to the spread of resistance genes that are mostly mutating rRNA around the ery binding site at the entrance to the protein exit tunnel. Additional effective resistance mechanisms include deletion or insertion mutations in ribosomal protein uL22, which lead to alterations of the exit tunnel shape, located 16 Å away from the drug's binding site. We determined the cryo-EM structures of the Staphylococcus aureus 70S ribosome, and its ery bound complex with a two amino acid deletion mutation in its ß hairpin loop, which grants the bacteria resistance to ery. The structures reveal that, although the binding of ery is stable, the movement of the flexible shorter uL22 loop towards the tunnel wall creates a wider path for nascent proteins, thus enabling bypass of the barrier formed by the drug. Moreover, upon drug binding, the tunnel widens further.


  • Organizational Affiliation

    The Weizmann Institute of Science, The Department of structural biology, Rehovot, 7610001, Israel.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2274Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for B3VKN3 (Staphylococcus aureus)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3215Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4206Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5175Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6175Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13145Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14122Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15146Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16137Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17120Staphylococcus aureusMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18119Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19114Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20116Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21102Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22110Staphylococcus aureusMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2389Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24103Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2594Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for A0A133Q8Z9 (Staphylococcus aureus)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2782Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for A0A077ULC5 (Staphylococcus schweitzeri)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2858Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for A0A077URJ8 (Staphylococcus schweitzeri)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2967Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for A0A077W1J5 (Staphylococcus schweitzeri)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3058Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for W8UVN7 (Staphylococcus aureus)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31 type B59Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for A0A380EL30 (Staphylococcus aureus)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3248Staphylococcus aureusMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33AA [auth 1]47Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for A0A077V2P0 (Staphylococcus schweitzeri)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34BA [auth 2]43Staphylococcus aureusMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35CA [auth 3]64Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for A0A077UL47 (Staphylococcus schweitzeri)
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36DA [auth 4]37Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for A0A077UGV8 (Staphylococcus schweitzeri)
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S ribosomal RNA2,905Staphylococcus aureus
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S ribosomal RNA115Staphylococcus aureus
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council322581
Danish National Research FoundationDenmark--

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-21
    Type: Initial release