6SPF

Pseudomonas aeruginosa 70s ribosome from an aminoglycoside resistant clinical isolate


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.89 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: https://doi.org/10.1073/pnas.1909831116
  • Primary Citation of Related Structures:  
    6SPB, 6SPC, 6SPD, 6SPE, 6SPF, 6SPG

  • 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 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.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2271Pseudomonas aeruginosaMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3207Pseudomonas aeruginosaMutation(s): 0 
UniProt
Find proteins for A0A072ZBZ2 (Pseudomonas aeruginosa)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4199Pseudomonas aeruginosaMutation(s): 0 
UniProt
Find proteins for A0A241XH26 (Pseudomonas aeruginosa)
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UniProt GroupA0A241XH26
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5174Pseudomonas aeruginosaMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6169Pseudomonas aeruginosaMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L978Pseudomonas aeruginosaMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11140Pseudomonas aeruginosaMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13141Pseudomonas aeruginosaMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14120Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15144Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16136Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17120Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18115Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19114Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20117Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21102Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22110Pseudomonas aeruginosaMutation(s): 0 
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Find proteins for A0A1C7BCP0 (Pseudomonas aeruginosa BL04)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2394Pseudomonas aeruginosaMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24103Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25188Pseudomonas aeruginosaMutation(s): 0 
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Find proteins for A0A072ZBM5 (Pseudomonas aeruginosa)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2776Pseudomonas aeruginosaMutation(s): 0 
UniProt
Find proteins for A0A071LFT4 (Pseudomonas aeruginosa)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2877Pseudomonas aeruginosaMutation(s): 0 
UniProt
Find proteins for A0A072ZIQ9 (Pseudomonas aeruginosa)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL2960Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3057Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31AA [auth 1]31Pseudomonas aeruginosaMutation(s): 0 
UniProt
Find proteins for A0A072ZJG4 (Pseudomonas aeruginosa)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32BA [auth 2]53Pseudomonas aeruginosaMutation(s): 0 
UniProt
Find proteins for A0A069QB25 (Pseudomonas aeruginosa)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33CA [auth 3]50Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34DA [auth 4]44Pseudomonas aeruginosaMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35EA [auth 5]63Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36FA [auth 6]38Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2HA [auth b]226Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3IA [auth c]203Pseudomonas aeruginosaMutation(s): 0 
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Find proteins for A0A140S919 (Pseudomonas aeruginosa)
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4JA [auth d]204Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5KA [auth e]150Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6LA [auth f]100Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7MA [auth g]154Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8NA [auth h]129Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9OA [auth i]126Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10PA [auth j]96Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11QA [auth k]115Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12RA [auth l]120Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13SA [auth m]110Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14TA [auth n]98Pseudomonas aeruginosaMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15UA [auth o]87Pseudomonas aeruginosaMutation(s): 0 
UniProt
Find proteins for A0A071L3R7 (Pseudomonas aeruginosa)
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16VA [auth p]78Pseudomonas aeruginosaMutation(s): 0 
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Find proteins for A0A2V4FRZ2 (Pseudomonas aeruginosa)
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17WA [auth q]76Pseudomonas aeruginosaMutation(s): 0 
UniProt
Find proteins for E2RXT5 (Pseudomonas aeruginosa)
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18XA [auth r]56Pseudomonas aeruginosaMutation(s): 0 
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Find proteins for A0A2V3DLV3 (Pseudomonas aeruginosa)
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UniProt GroupA0A2V3DLV3
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19YA [auth s]80Pseudomonas aeruginosaMutation(s): 0 
UniProt
Find proteins for E2RXT2 (Pseudomonas aeruginosa)
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UniProt GroupE2RXT2
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20ZA [auth t]86Pseudomonas aeruginosaMutation(s): 0 
UniProt
Find proteins for A0A072ZDZ9 (Pseudomonas aeruginosa)
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21AB [auth u]34Pseudomonas aeruginosaMutation(s): 0 
UniProt
Find proteins for A0A069QC99 (Pseudomonas aeruginosa)
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UniProt GroupA0A069QC99
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Entity ID: 1
MoleculeChains LengthOrganismImage
Pseudomonas aeruginosa strain PAO1 23S ribosomal RNA2,888Pseudomonas aeruginosa
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S rRNA117Pseudomonas aeruginosa
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Entity ID: 33
MoleculeChains LengthOrganismImage
16S rRNAGA [auth a]1,521Pseudomonas aeruginosa
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.89 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



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  (Full details and data files)

  • Version 1.0: 2019-10-23
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Database references
  • Version 1.2: 2020-07-29
    Changes: Database references