ISDA

Deposition Date 2019-09-01

Release Date 2019-10-23

Last Version Date 2024-10-16

Entry Detail

PDB ID:

6SPF

Keywords:

RIBOSOME

Title:

Pseudomonas aeruginosa 70s ribosome from an aminoglycoside resistant clinical isolate

Biological Source:

Source Organism:

Pseudomonas aeruginosa (Taxon ID: 287)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

2.89 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:AA (auth: 1)
Chain Length:31
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:A0A072ZJG4 Pfam ID:PF01197

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:BA (auth: 2)
Chain Length:53
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:A0A069QB25 Pfam ID:PF01783

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:CA (auth: 3)
Chain Length:50
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:A0A140SG33 Pfam ID:PF00471

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:DA (auth: 4)
Chain Length:44
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:A0A087L9L7 Pfam ID:PF00468

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:EA (auth: 5)
Chain Length:63
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:A0A069QC44 Pfam ID:PF01632

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:FA (auth: 6)
Chain Length:38
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:E2RXU2 Pfam ID:PF00444

Polymer Type:polyribonucleotide
Molecule:Pseudomonas aeruginosa strain PAO1 23S ribosomal RNA
Chain IDs:A
Chain Length:2888
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:B
Chain Length:117
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:C
Chain Length:271
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:A0A241XHA2 Pfam ID:PF00181, PF03947

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:D
Chain Length:207
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:A0A072ZBZ2 Pfam ID:PF00297

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:E
Chain Length:150
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:A0A241XH26 Pfam ID:PF00573

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:F
Chain Length:174
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:A0A072ZMU2 Pfam ID:PF00281, PF00673

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Mutations:Delta 92GYKA
Chain IDs:G
Chain Length:169
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:A0A2V3F3S9 Pfam ID:PF00347

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:H
Chain Length:129
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:A0A072ZKF0 Pfam ID:PF01281

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Gene (Uniprot):rplK
Chain IDs:I
Chain Length:140
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:A0A2V3GYK0 Pfam ID:PF03946, PF00298

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:J
Chain Length:141
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:A0A071L356 Pfam ID:PF00572

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:K
Chain Length:115
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:E2RXT6 Pfam ID:PF00238

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:L
Chain Length:120
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:A0A2V3D5Z8 Pfam ID:PF00828

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:M
Chain Length:110
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:A0A069QEB6 Pfam ID:PF00252

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:N
Chain Length:98
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:A0A072ZCA1 Pfam ID:PF01196

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:O
Chain Length:87
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:E2RXU0 Pfam ID:PF00861

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:P
Chain Length:78
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:A0A263PZC6 Pfam ID:PF01245

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:Q
Chain Length:117
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:A0A069QEE3 Pfam ID:PF00453

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:R
Chain Length:56
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:A0A072ZDZ0 Pfam ID:PF00829

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Chain IDs:S
Chain Length:110
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:T
Chain Length:86
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:E2RXT1 Pfam ID:PF00276

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:U
Chain Length:34
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:E2RXT7 Pfam ID:PF00467, PF17136

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:V
Chain Length:188
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:A0A072ZBM5 Pfam ID:PF01386, PF14693

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:W
Chain Length:76
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:A0A071LFT4 Pfam ID:PF01016

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:X
Chain Length:77
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:A0A072ZIQ9 Pfam ID:PF00830

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL29
Chain IDs:Y
Chain Length:60
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:Z
Chain Length:57
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:E2RXU1 Pfam ID:PF00327

Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:GA (auth: a)
Chain Length:2888
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:HA (auth: b)
Chain Length:117
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:A0A072ZPV8 Pfam ID:PF00318

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:IA (auth: c)
Chain Length:271
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:A0A140S919 Pfam ID:PF07650, PF00189

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:JA (auth: d)
Chain Length:207
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:A0A072ZDF7 Pfam ID:PF00163, PF01479

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:KA (auth: e)
Chain Length:150
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:A0A241XG65 Pfam ID:PF00333, PF03719

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:LA (auth: f)
Chain Length:174
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:A0A069Q263 Pfam ID:PF01250

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:MA (auth: g)
Chain Length:169
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:A0A2V3F2U6 Pfam ID:PF00177

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:NA (auth: h)
Chain Length:129
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:E2RXT9 Pfam ID:PF00410

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:OA (auth: i)
Chain Length:140
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:A0A069PXX1 Pfam ID:PF00380

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:PA (auth: j)
Chain Length:141
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:E2RXT0 Pfam ID:PF00338

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:QA (auth: k)
Chain Length:115
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:E2RXU4 Pfam ID:PF00411

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:RA (auth: l)
Chain Length:120
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:A0A071L394 Pfam ID:PF00164

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:SA (auth: m)
Chain Length:110
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:E2RXU3 Pfam ID:PF00416

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Gene (Uniprot):rpsN
Chain IDs:TA (auth: n)
Chain Length:98
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:E2RXT8 Pfam ID:PF00253

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:UA (auth: o)
Chain Length:87
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:A0A071L3R7 Pfam ID:PF00312

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:VA (auth: p)
Chain Length:78
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:A0A2V4FRZ2 Pfam ID:PF00886

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:WA (auth: q)
Chain Length:117
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:E2RXT5 Pfam ID:PF00366

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:XA (auth: r)
Chain Length:56
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:A0A2V3DLV3 Pfam ID:PF01084

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:YA (auth: s)
Chain Length:110
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:E2RXT2 Pfam ID:PF00203

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:ZA (auth: t)
Chain Length:86
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:A0A072ZDZ9 Pfam ID:PF01649

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S21
Gene (Uniprot):rpsU
Chain IDs:AB (auth: u)
Chain Length:34
Number of Molecules:1
Biological Source:Pseudomonas aeruginosa

UniProt ID:A0A069QC99 Pfam ID:PF01165

Ligand Molecules

Primary Citation

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.Show

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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Protein

Chemical

Disease

Primary Citation of related structures