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.USA 116: 22275-22281

  • DOI: 10.1073/pnas.1909831116
  • Primary Citation of Related Structures:  

  • 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.,The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.,Department of Structural Biology, The Weizmann Institute of Science, 7610001 Rehovot, Israel; sm@bio.dtu.dk ada.yonath@weizmann.ac.il.,Department of Clinical Microbiology, Rigshospitalet, 2100 Copenhagen, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 1165 Copenhagen, Denmark.,Biomedicine Discovery Institute, Department of Microbiology, Monash University, 3800 Clayton, VIC, Australia.,The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; sm@bio.dtu.dk ada.yonath@weizmann.ac.il.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
b
221Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rpsB (rpsB_2)
Find proteins for A0A072ZPV8 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A072ZPV8
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
c
203Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rpsC (rpsC_2)
Find proteins for A0A140S919 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A140S919
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
d
205Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rpsD (rpsD_2)
Find proteins for A0A072ZDF7 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A072ZDF7
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
e
149Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rpsE (rpsE_2)
Find proteins for A0A241XG65 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A241XG65
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
f
100Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rpsF (rpsF_1)
Find proteins for A0A069Q263 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A069Q263
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
g
154Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rpsG_2 (rpsG)
Find proteins for A0A2V3F2U6 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A2V3F2U6
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
h
125Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rpsH_2 (rpsH)
Find proteins for E2RXT9 (Pseudomonas aeruginosa)
Go to UniProtKB:  E2RXT9
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
i
126Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rpsI (rpsI_1)
Find proteins for A0A069PXX1 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A069PXX1
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
j
96Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rpsJ_2 (rpsJ)
Find proteins for E2RXT0 (Pseudomonas aeruginosa)
Go to UniProtKB:  E2RXT0
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
k
115Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rpsK (rpsK_2)
Find proteins for E2RXU4 (Pseudomonas aeruginosa)
Go to UniProtKB:  E2RXU4
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
l
120Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rpsL (rpsL_2)
Find proteins for A0A071L394 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A071L394
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
m
109Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rpsM_2 (rpsM)
Find proteins for E2RXU3 (Pseudomonas aeruginosa)
Go to UniProtKB:  E2RXU3
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
n
98Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rpsN_2 (rpsN)
Find proteins for E2RXT8 (Pseudomonas aeruginosa)
Go to UniProtKB:  E2RXT8
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
o
87Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rpsO (rpsO_2)
Find proteins for A0A071L3R7 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A071L3R7
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
p
78Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rpsP (rpsP_1)
Find proteins for A0A2V4FRZ2 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A2V4FRZ2
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
q
76Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rpsQ (rpsQ_2)
Find proteins for E2RXT5 (Pseudomonas aeruginosa)
Go to UniProtKB:  E2RXT5
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
r
56Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rpsR (rpsR_1)
Find proteins for A0A2V3DLV3 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A2V3DLV3
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
s
80Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rpsS_2 (rpsS)
Find proteins for E2RXT2 (Pseudomonas aeruginosa)
Go to UniProtKB:  E2RXT2
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
t
86Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rpsT (rpsT_1)
Find proteins for A0A072ZDZ9 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A072ZDZ9
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
u
34Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rpsU (rpsU_1)
Find proteins for A0A069QC99 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A069QC99
Entity ID: 1
MoleculeChainsLengthOrganism
16S rRNAa1519Pseudomonas aeruginosa
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Data collection, Database references
  • Version 1.2: 2019-11-06
    Type: Data collection, Database references