6SPF image
Entry Detail
PDB ID:
6SPF
EMDB ID:
Keywords:
Title:
Pseudomonas aeruginosa 70s ribosome from an aminoglycoside resistant clinical isolate
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2019-09-01
Release Date:
2019-10-23
Method Details:
Experimental Method:
Resolution:
2.89 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L31
Chain IDs:AA (auth: 1)
Chain Length:31
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L32
Chain IDs:BA (auth: 2)
Chain Length:53
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L33
Chain IDs:CA (auth: 3)
Chain Length:50
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L34
Chain IDs:DA (auth: 4)
Chain Length:44
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L35
Chain IDs:EA (auth: 5)
Chain Length:63
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L36
Chain IDs:FA (auth: 6)
Chain Length:38
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polyribonucleotide
Description:Pseudomonas aeruginosa strain PAO1 23S ribosomal RNA
Chain IDs:A
Chain Length:2888
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polyribonucleotide
Description:5S rRNA
Chain IDs:B
Chain Length:117
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L2
Chain IDs:C
Chain Length:271
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L3
Chain IDs:D
Chain Length:207
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L4
Chain IDs:E
Chain Length:150
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L5
Chain IDs:F
Chain Length:174
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L6
Mutations:Delta 92GYKA
Chain IDs:G
Chain Length:169
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L9
Chain IDs:H
Chain Length:129
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L11
Chain IDs:I
Chain Length:140
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L13
Chain IDs:J
Chain Length:141
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L14
Chain IDs:K
Chain Length:115
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L15
Chain IDs:L
Chain Length:120
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L16
Chain IDs:M
Chain Length:110
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L17
Chain IDs:N
Chain Length:98
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L18
Chain IDs:O
Chain Length:87
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L19
Chain IDs:P
Chain Length:78
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L20
Chain IDs:Q
Chain Length:117
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L21
Chain IDs:R
Chain Length:56
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L22
Chain IDs:S
Chain Length:110
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L23
Chain IDs:T
Chain Length:86
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L24
Chain IDs:U
Chain Length:34
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L25
Chain IDs:V
Chain Length:188
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L27
Chain IDs:W
Chain Length:76
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L28
Chain IDs:X
Chain Length:77
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:Ribosomal protein uL29
Chain IDs:Y
Chain Length:60
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L30
Chain IDs:Z
Chain Length:57
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polyribonucleotide
Description:16S rRNA
Chain IDs:GA (auth: a)
Chain Length:2888
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S2
Chain IDs:HA (auth: b)
Chain Length:117
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S3
Chain IDs:IA (auth: c)
Chain Length:271
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S4
Chain IDs:JA (auth: d)
Chain Length:207
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S5
Chain IDs:KA (auth: e)
Chain Length:150
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S6
Chain IDs:LA (auth: f)
Chain Length:174
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S7
Chain IDs:MA (auth: g)
Chain Length:169
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S8
Chain IDs:NA (auth: h)
Chain Length:129
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S9
Chain IDs:OA (auth: i)
Chain Length:140
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S10
Chain IDs:PA (auth: j)
Chain Length:141
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S11
Chain IDs:QA (auth: k)
Chain Length:115
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S12
Chain IDs:RA (auth: l)
Chain Length:120
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S13
Chain IDs:SA (auth: m)
Chain Length:110
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S14
Chain IDs:TA (auth: n)
Chain Length:98
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S15
Chain IDs:UA (auth: o)
Chain Length:87
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S16
Chain IDs:VA (auth: p)
Chain Length:78
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S17
Chain IDs:WA (auth: q)
Chain Length:117
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S18
Chain IDs:XA (auth: r)
Chain Length:56
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S19
Chain IDs:YA (auth: s)
Chain Length:110
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S20
Chain IDs:ZA (auth: t)
Chain Length:86
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S21
Chain IDs:AB (auth: u)
Chain Length:34
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa
Ligand Molecules
Primary Citation
Structure ofPseudomonas aeruginosaribosomes from an aminoglycoside-resistant clinical isolate.
Proc.Natl.Acad.Sci.USA 116 22275 22281 (2019)
PMID: 31611393 DOI: 10.1073/pnas.1909831116

Abstact

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.

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Disease

Primary Citation of related structures