6SPC

Pseudomonas aeruginosa 30s ribosome from an aminoglycoside resistant clinical isolate


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.95 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

Structure ofPseudomonas aeruginosaribosomes from an aminoglycoside-resistant clinical isolate.

Halfon, Y.Jimenez-Fernandez, A.La Rosa, R.Espinosa Portero, R.Krogh Johansen, H.Matzov, D.Eyal, Z.Bashan, A.Zimmerman, E.Belousoff, M.Molin, S.Yonath, A.

(2019) Proc Natl Acad Sci U S A 116: 22275-22281

  • DOI: 10.1073/pnas.1909831116
  • Primary Citation of Related Structures:  
    6SPD, 6SPC, 6SPF, 6SPE, 6SPG, 6SPB

  • PubMed Abstract: 
  • Resistance to antibiotics has become a major threat to modern medicine. The ribosome plays a fundamental role in cell vitality by the translation of the genetic code into proteins; hence, it is a major target for clinically useful antibiotics. We rep ...

    Resistance to antibiotics has become a major threat to modern medicine. The ribosome plays a fundamental role in cell vitality by the translation of the genetic code into proteins; hence, it is a major target for clinically useful antibiotics. We report here the cryo-electron microscopy structures of the ribosome of a pathogenic aminoglycoside (AG)-resistant Pseudomonas aeruginosa strain, as well as of a nonresistance strain isolated from a cystic fibrosis patient. The structural studies disclosed defective ribosome complex formation due to a conformational change of rRNA helix H69, an essential intersubunit bridge, and a secondary binding site of the AGs. In addition, a stable conformation of nucleotides A1486 and A1487, pointing into helix h44, is created compared to a non-AG-bound ribosome. We suggest that altering the conformations of ribosomal protein uL6 and rRNA helix H69, which interact with initiation-factor IF2, interferes with proper protein synthesis initiation.


    Organizational Affiliation

    Department of Structural Biology, The Weizmann Institute of Science, 7610001 Rehovot, Israel; sm@bio.dtu.dk ada.yonath@weizmann.ac.il.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2b221Pseudomonas aeruginosaMutation(s): 0 
Gene Names: 
Find proteins for A0A072ZPV8 (Pseudomonas aeruginosa)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3c203Pseudomonas aeruginosaMutation(s): 0 
Gene Names: 
Find proteins for A0A140S919 (Pseudomonas aeruginosa)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4d205Pseudomonas aeruginosaMutation(s): 0 
Gene Names: 
Find proteins for A0A072ZDF7 (Pseudomonas aeruginosa)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5e149Pseudomonas aeruginosaMutation(s): 0 
Gene Names: 
Find proteins for A0A241XG65 (Pseudomonas aeruginosa)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6f100Pseudomonas aeruginosaMutation(s): 0 
Gene Names: 
Find proteins for A0A069Q263 (Pseudomonas aeruginosa)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7g154Pseudomonas aeruginosaMutation(s): 0 
Gene Names: 
Find proteins for A0A2V3F2U6 (Pseudomonas aeruginosa)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8h125Pseudomonas aeruginosaMutation(s): 0 
Gene Names: 
Find proteins for E2RXT9 (Pseudomonas aeruginosa)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9i126Pseudomonas aeruginosaMutation(s): 0 
Gene Names: 
Find proteins for A0A069PXX1 (Pseudomonas aeruginosa)
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Entity ID: 10
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30S ribosomal protein S10j96Pseudomonas aeruginosaMutation(s): 0 
Gene Names: 
Find proteins for E2RXT0 (Pseudomonas aeruginosa)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11k115Pseudomonas aeruginosaMutation(s): 0 
Gene Names: 
Find proteins for E2RXU4 (Pseudomonas aeruginosa)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12l120Pseudomonas aeruginosaMutation(s): 0 
Gene Names: 
Find proteins for A0A071L394 (Pseudomonas aeruginosa)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13m109Pseudomonas aeruginosaMutation(s): 0 
Gene Names: 
Find proteins for E2RXU3 (Pseudomonas aeruginosa)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14n98Pseudomonas aeruginosaMutation(s): 0 
Gene Names: 
Find proteins for E2RXT8 (Pseudomonas aeruginosa)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15o87Pseudomonas aeruginosaMutation(s): 0 
Gene Names: 
Find proteins for A0A071L3R7 (Pseudomonas aeruginosa)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16p78Pseudomonas aeruginosaMutation(s): 0 
Gene Names: 
Find proteins for A0A2V4FRZ2 (Pseudomonas aeruginosa)
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17q76Pseudomonas aeruginosaMutation(s): 0 
Gene Names: 
Find proteins for E2RXT5 (Pseudomonas aeruginosa)
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18r56Pseudomonas aeruginosaMutation(s): 0 
Gene Names: 
Find proteins for A0A2V3DLV3 (Pseudomonas aeruginosa)
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19s80Pseudomonas aeruginosaMutation(s): 0 
Gene Names: 
Find proteins for E2RXT2 (Pseudomonas aeruginosa)
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20t86Pseudomonas aeruginosaMutation(s): 0 
Gene Names: 
Find proteins for A0A072ZDZ9 (Pseudomonas aeruginosa)
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S21u34Pseudomonas aeruginosaMutation(s): 0 
Gene Names: 
Find proteins for A0A069QC99 (Pseudomonas aeruginosa)
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S rRNAa1519Pseudomonas aeruginosa
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.95 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Danish Council for Independent ResearchDenmarkDFF-4181-00115
Novo Nordisk FoundationDenmark--
European Research Council322581
European UnioniNEXT, project number 653706, funded by the Horizon 2020 programme of the European Union

Revision History 

  • Version 1.0: 2019-10-16
    Type: Initial release
  • Version 1.1: 2019-10-23
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-06
    Changes: Data collection, Database references