6SPB

Pseudomonas aeruginosa 50s ribosome from a clinical isolate with a mutation in uL6


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.82 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: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
C
271Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rplB
Find proteins for A0A241XHA2 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A241XHA2
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
D
207Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rplC
Find proteins for A0A072ZBZ2 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A072ZBZ2
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
E
199Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rplD
Find proteins for A0A241XH26 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A241XH26
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
F
174Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rplE
Find proteins for A0A072ZMU2 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A072ZMU2
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
G
169Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rplF
Find proteins for A0A2V3F3S9 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A2V3F3S9
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
H
78Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rplI
Find proteins for A0A072ZKF0 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A072ZKF0
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
I
140Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rplK
Find proteins for A0A2V3GYK0 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A2V3GYK0
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
J
141Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rplM
Find proteins for A0A071L356 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A071L356
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
K
120Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rplN
Find proteins for E2RXT6 (Pseudomonas aeruginosa)
Go to UniProtKB:  E2RXT6
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
L
144Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rplO
Find proteins for A0A2V3D5Z8 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A2V3D5Z8
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
M
136Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rplP
Find proteins for A0A069QEB6 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A069QEB6
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
N
120Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rplQ
Find proteins for A0A072ZCA1 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A072ZCA1
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
O
115Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rplR
Find proteins for E2RXU0 (Pseudomonas aeruginosa)
Go to UniProtKB:  E2RXU0
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
P
115Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rplS
Find proteins for A0A263PZC6 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A263PZC6
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
Q
117Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rplT
Find proteins for A0A069QEE3 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A069QEE3
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
R
102Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rplU
Find proteins for A0A072ZDZ0 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A072ZDZ0
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
S
110Pseudomonas aeruginosa BL04Mutation(s): 0 
Gene Names: rplV
Find proteins for A0A1C7BCP0 (Pseudomonas aeruginosa BL04)
Go to UniProtKB:  A0A1C7BCP0
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
T
94Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rplW
Find proteins for E2RXT1 (Pseudomonas aeruginosa)
Go to UniProtKB:  E2RXT1
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
U
103Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rplX
Find proteins for E2RXT7 (Pseudomonas aeruginosa)
Go to UniProtKB:  E2RXT7
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
V
188Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rplY (ctc)
Find proteins for A0A072ZBM5 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A072ZBM5
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
W
76Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rpmA
Find proteins for A0A071LFT4 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A071LFT4
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
X
77Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rpmB
Find proteins for A0A072ZIQ9 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A072ZIQ9
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
Y
60Pseudomonas sp. (strain GM41(2012))Mutation(s): 0 
Gene Names: rpmC
Find proteins for W6V2V8 (Pseudomonas sp. (strain GM41(2012)))
Go to UniProtKB:  W6V2V8
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
Z
57Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rpmD
Find proteins for E2RXU1 (Pseudomonas aeruginosa)
Go to UniProtKB:  E2RXU1
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
1
31Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rpmE
Find proteins for A0A072ZJG4 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A072ZJG4
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
2
53Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rpmF
Find proteins for A0A069QB25 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A069QB25
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
3
50Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rpmG
Find proteins for A0A140SG33 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A140SG33
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
4
44Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rpmH
Find proteins for A0A087L9L7 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A087L9L7
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
5
63Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rpmI
Find proteins for A0A069QC44 (Pseudomonas aeruginosa)
Go to UniProtKB:  A0A069QC44
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
6
38Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rpmJ
Find proteins for E2RXU2 (Pseudomonas aeruginosa)
Go to UniProtKB:  E2RXU2
Entity ID: 1
MoleculeChainsLengthOrganism
23S ribosomal RNAA2888Pseudomonas aeruginosa
Entity ID: 2
MoleculeChainsLengthOrganism
5S rRNAB117Pseudomonas aeruginosa
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.82 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