PDBsum entry 6spd

Ribosome

PDB id: 6spd

Contents

Protein chains

271 a.a.

207 a.a.

199 a.a.

175 a.a.

173 a.a.

147 a.a.

140 a.a.

141 a.a.

120 a.a.

143 a.a.

135 a.a.

118 a.a.

115 a.a.

113 a.a.

117 a.a.

103 a.a.

109 a.a.

92 a.a.

103 a.a.

188 a.a.

76 a.a.

77 a.a.

60 a.a.

57 a.a.

31 a.a.

53 a.a.

50 a.a.

44 a.a.

63 a.a.

38 a.a.

DNA/RNA

PDB id:

6spd

Name:

Ribosome

Title:

Pseudomonas aeruginosa 50s ribosome from a clinical isolate

Structure:

23s ribosomal RNA. Chain: a. 5s ribosomal RNA. Chain: b. 50s ribosomal protein l2. Chain: c. 50s ribosomal protein l3. Chain: d. 50s ribosomal protein l4.

Source:

Pseudomonas aeruginosa. Organism_taxid: 287. Organism_taxid: 287

Authors:

Y.Halfon,A.Jimenez-Fernande,R.La Ros,R.Espinos,H.Krogh Johansen, D.Matzov,Z.Eyal,A.Bashan,E.Zimmerman,M.Belousoff,S.Molin,A.Yonath

Key ref:

Y.Halfon et al. (2019). Structure of Pseudomonas aeruginosa ribosomes from an aminoglycoside-resistant clinical isolate. Proc Natl Acad Sci U S A, 116, 22275-22281. PubMed id: 31611393 DOI: 10.1073/pnas.1909831116

Date:

01-Sep-19 Release date: 16-Oct-19

Protein chain

A0A241XHA2  (A0A241XHA2_PSEAI) -  Large ribosomal subunit protein uL2 from Pseudomonas aeruginosa

Seq: 273 a.a.

Struc: 271 a.a.

Protein chain

A0A072ZBZ2  (A0A072ZBZ2_PSEAI) -  Large ribosomal subunit protein uL3 from Pseudomonas aeruginosa

Seq: 211 a.a.

Struc: 207 a.a.

Protein chain

A0A241XH26  (A0A241XH26_PSEAI) -  Large ribosomal subunit protein uL4 from Pseudomonas aeruginosa

Seq: 200 a.a.

Struc: 199 a.a.

Protein chain

A0A072ZMU2  (A0A072ZMU2_PSEAI) -  Large ribosomal subunit protein uL5 from Pseudomonas aeruginosa

Seq: 179 a.a.

Struc: 175 a.a.*

Protein chain

A0A2V3F3S9  (A0A2V3F3S9_PSEAI) -  Large ribosomal subunit protein uL6 from Pseudomonas aeruginosa

Seq: 177 a.a.

Struc: 173 a.a.

Protein chain

A0A072ZKF0  (A0A072ZKF0_PSEAI) -  Large ribosomal subunit protein bL9 from Pseudomonas aeruginosa

Seq: 148 a.a.

Struc: 147 a.a.

Protein chain

A0A2V3GYK0  (A0A2V3GYK0_PSEAI) -  Large ribosomal subunit protein uL11 from Pseudomonas aeruginosa

Seq: 143 a.a.

Struc: 140 a.a.

Protein chain

A0A071L356  (A0A071L356_PSEAI) -  Large ribosomal subunit protein uL13 from Pseudomonas aeruginosa

Seq: 142 a.a.

Struc: 141 a.a.

Protein chain

E2RXT6  (E2RXT6_PSEAI) -  Large ribosomal subunit protein uL14 from Pseudomonas aeruginosa

Seq: 122 a.a.

Struc: 120 a.a.

Protein chain

A0A2V3D5Z8  (A0A2V3D5Z8_PSEAI) -  Large ribosomal subunit protein uL15 from Pseudomonas aeruginosa

Seq: 144 a.a.

Struc: 143 a.a.

Protein chain

A0A069QEB6  (A0A069QEB6_PSEAI) -  Large ribosomal subunit protein uL16 from Pseudomonas aeruginosa

Seq: 137 a.a.

Struc: 135 a.a.

Protein chain

A0A072ZCA1  (A0A072ZCA1_PSEAI) -  Large ribosomal subunit protein bL17 from Pseudomonas aeruginosa

Seq: 129 a.a.

Struc: 118 a.a.

Protein chain

E2RXU0  (E2RXU0_PSEAI) -  Large ribosomal subunit protein uL18 from Pseudomonas aeruginosa

Seq: 116 a.a.

Struc: 115 a.a.

Protein chain

A0A263PZC6  (A0A263PZC6_PSEAI) -  Large ribosomal subunit protein bL19 from Pseudomonas aeruginosa

Seq: 116 a.a.

Struc: 113 a.a.

Protein chain

A0A069QEE3  (A0A069QEE3_PSEAI) -  Large ribosomal subunit protein bL20 from Pseudomonas aeruginosa

Seq: 118 a.a.

Struc: 117 a.a.

Protein chain

A0A072ZDZ0  (A0A072ZDZ0_PSEAI) -  Large ribosomal subunit protein bL21 from Pseudomonas aeruginosa

Seq: 103 a.a.

Struc: 103 a.a.

Protein chain

No UniProt id for this chain

Struc: 109 a.a.

Protein chain

E2RXT1  (E2RXT1_PSEAI) -  Large ribosomal subunit protein uL23 from Pseudomonas aeruginosa

Seq: 99 a.a.

Struc: 92 a.a.

Protein chain

E2RXT7  (E2RXT7_PSEAI) -  Large ribosomal subunit protein uL24 from Pseudomonas aeruginosa

Seq: 104 a.a.

Struc: 103 a.a.

Protein chain

A0A072ZBM5  (A0A072ZBM5_PSEAI) -  Large ribosomal subunit protein bL25 from Pseudomonas aeruginosa

Seq: 204 a.a.

Struc: 188 a.a.*

Protein chain

A0A071LFT4  (A0A071LFT4_PSEAI) -  Large ribosomal subunit protein bL27 from Pseudomonas aeruginosa

Seq: 85 a.a.

Struc: 76 a.a.*

Protein chain

A0A072ZIQ9  (A0A072ZIQ9_PSEAI) -  Large ribosomal subunit protein bL28 from Pseudomonas aeruginosa

Seq: 78 a.a.

Struc: 77 a.a.

Protein chain

No UniProt id for this chain

Struc: 60 a.a.

Protein chain

E2RXU1  (E2RXU1_PSEAI) -  Large ribosomal subunit protein uL30 from Pseudomonas aeruginosa

Seq: 58 a.a.

Struc: 57 a.a.

Protein chain

A0A072ZJG4  (A0A072ZJG4_PSEAI) -  Large ribosomal subunit protein bL31 from Pseudomonas aeruginosa

Seq: 71 a.a.

Struc: 31 a.a.

Protein chain

A0A069QB25  (A0A069QB25_PSEAI) -  Large ribosomal subunit protein bL32 from Pseudomonas aeruginosa

Seq: 60 a.a.

Struc: 53 a.a.

Protein chain

A0A140SG33  (A0A140SG33_PSEAI) -  Large ribosomal subunit protein bL33 from Pseudomonas aeruginosa

Seq: 51 a.a.

Struc: 50 a.a.

Protein chain

A0A087L9L7  (A0A087L9L7_PSEAI) -  Large ribosomal subunit protein bL34 from Pseudomonas aeruginosa

Seq: 44 a.a.

Struc: 44 a.a.

Protein chain

A0A069QC44  (A0A069QC44_PSEAI) -  Large ribosomal subunit protein bL35 from Pseudomonas aeruginosa

Seq: 64 a.a.

Struc: 63 a.a.

Protein chain

E2RXU2  (E2RXU2_PSEAI) -  Large ribosomal subunit protein bL36 from Pseudomonas aeruginosa

Seq: 38 a.a.

Struc: 38 a.a.

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

DNA/RNA chains

G-U-C-A-A-G-U-G-A-A-G-A-A-G-C-G-C-A-U-A-C-G-G-U-G-G-A-U-G-C-C-U-U-G-G-C-A-G-U- ... 2851 bases

U-U-G-A-C-G-A-U-C-A-U-A-G-A-G-C-G-U-U-G-G-A-A-C-C-A-C-C-U-G-A-U-C-C-C-U-U-C-C- 116 bases

DOI no: 10.1073/pnas.1909831116

Proc Natl Acad Sci U S A 116:22275-22281 (2019)

PubMed id: 31611393

Structure of Pseudomonas aeruginosa ribosomes from an aminoglycoside-resistant clinical isolate.

Y.Halfon, A.Jimenez-Fernandez, R.La Rosa, R.Espinosa Portero, H.Krogh Johansen, D.Matzov, Z.Eyal, A.Bashan, E.Zimmerman, M.Belousoff, S.Molin, A.Yonath.

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.