PDBsum entry 4tpc

Ribosome

PDB id: 4tpc

Contents

Protein chains

218 a.a.

206 a.a.

205 a.a.

150 a.a.

100 a.a.

151 a.a.

129 a.a.

127 a.a.

98 a.a.

117 a.a.

123 a.a.

114 a.a.

96 a.a.

88 a.a.

82 a.a.

80 a.a.

55 a.a.

79 a.a.

85 a.a.

51 a.a.

DNA/RNA

Metals

_MG ×72

Waters ×203

Obsolete entry

PDB id:

4tpc

Name:

Ribosome

Title:

Crystal structure of the e. Coli ribosome bound to flopristin and linopristin. This file contains the 30s subunit of the first 70s ribosome.

Structure:

16s rrna. Chain: a. 30s ribosomal protein s2. Chain: b. 30s ribosomal protein s3. Chain: c. 30s ribosomal protein s4. Chain: d. 30s ribosomal protein s5.

Source:

Escherichia coli str. K-12 substr. Mds42. Organism_taxid: 1110693. Escherichia coli. Organism_taxid: 83333. Strain: k12. Strain: k12

Resolution:

2.80Å R-factor: 0.216 R-free: 0.260

Authors:

J.Noeske,J.Huang,N.B.Olivier,R.A.Giacobbe,M.Zambrowski,J.H.D.Cate

Key ref:

J.Noeske et al. (2014). Synergy of streptogramin antibiotics occurs independently of their effects on translation. Antimicrob Agents Chemother, 58, 5269-5279. PubMed id: 24957822 DOI: 10.1128/AAC.03389-14

Date:

07-Jun-14 Release date: 30-Jul-14

Protein chain

P0A7V0  (RS2_ECOLI) -  30S ribosomal protein S2 from Escherichia coli (strain K12)

Seq: 241 a.a.

Struc: 218 a.a.

Protein chain

P0A7V3  (RS3_ECOLI) -  30S ribosomal protein S3 from Escherichia coli (strain K12)

Seq: 233 a.a.

Struc: 206 a.a.

Protein chain

P0A7V8  (RS4_ECOLI) -  30S ribosomal protein S4 from Escherichia coli (strain K12)

Seq: 206 a.a.

Struc: 205 a.a.

Protein chain

P0A7W1  (RS5_ECOLI) -  30S ribosomal protein S5 from Escherichia coli (strain K12)

Seq: 167 a.a.

Struc: 150 a.a.

Protein chain

P02358  (RS6_ECOLI) -  30S ribosomal protein S6 from Escherichia coli (strain K12)

Seq: 135 a.a.

Struc: 100 a.a.

Protein chain

P02359  (RS7_ECOLI) -  30S ribosomal protein S7 from Escherichia coli (strain K12)

Seq: 179 a.a.

Struc: 151 a.a.

Protein chain

P0A7W7  (RS8_ECOLI) -  30S ribosomal protein S8 from Escherichia coli (strain K12)

Seq: 130 a.a.

Struc: 129 a.a.

Protein chain

P0A7X3  (RS9_ECOLI) -  30S ribosomal protein S9 from Escherichia coli (strain K12)

Seq: 130 a.a.

Struc: 127 a.a.

Protein chain

P0A7R5  (RS10_ECOLI) -  30S ribosomal protein S10 from Escherichia coli (strain K12)

Seq: 103 a.a.

Struc: 98 a.a.

Protein chain

P0A7R9  (RS11_ECOLI) -  30S ribosomal protein S11 from Escherichia coli (strain K12)

Seq: 129 a.a.

Struc: 117 a.a.

Protein chain

P0A7S3  (RS12_ECOLI) -  30S ribosomal protein S12 from Escherichia coli (strain K12)

Seq: 124 a.a.

Struc: 123 a.a.

Protein chain

P0A7S9  (RS13_ECOLI) -  30S ribosomal protein S13 from Escherichia coli (strain K12)

Seq: 118 a.a.

Struc: 114 a.a.

Protein chain

P0AG59  (RS14_ECOLI) -  30S ribosomal protein S14 from Escherichia coli (strain K12)

Seq: 101 a.a.

Struc: 96 a.a.

Protein chain

P0ADZ4  (RS15_ECOLI) -  30S ribosomal protein S15 from Escherichia coli (strain K12)

Seq: 89 a.a.

Struc: 88 a.a.

Protein chain

P0A7T3  (RS16_ECOLI) -  30S ribosomal protein S16 from Escherichia coli (strain K12)

Seq: 82 a.a.

Struc: 82 a.a.

Protein chain

P0AG63  (RS17_ECOLI) -  30S ribosomal protein S17 from Escherichia coli (strain K12)

Seq: 84 a.a.

Struc: 80 a.a.

Protein chain

P0A7T7  (RS18_ECOLI) -  30S ribosomal protein S18 from Escherichia coli (strain K12)

Seq: 75 a.a.

Struc: 55 a.a.

Protein chain

P0A7U3  (RS19_ECOLI) -  30S ribosomal protein S19 from Escherichia coli (strain K12)

Seq: 92 a.a.

Struc: 79 a.a.

Protein chain

P0A7U7  (RS20_ECOLI) -  30S ribosomal protein S20 from Escherichia coli (strain K12)

Seq: 87 a.a.

Struc: 85 a.a.

Protein chain

P68679  (RS21_ECOLI) -  30S ribosomal protein S21 from Escherichia coli (strain K12)

Seq: 71 a.a.

Struc: 51 a.a.

DNA/RNA chain

A-A-U-U-G-A-A-G-A-G-U-U-U-G-A-U-C-A-U-G-G-C-U-C-A-G-A-U-U-G-A-A-C-G-C-U-G-G-C- ... 1538 bases

DOI no: 10.1128/AAC.03389-14

Antimicrob Agents Chemother 58:5269-5279 (2014)

PubMed id: 24957822

Synergy of streptogramin antibiotics occurs independently of their effects on translation.

J.Noeske, J.Huang, N.B.Olivier, R.A.Giacobbe, M.Zambrowski, J.H.Cate.

ABSTRACT

Streptogramin antibiotics are divided into types A and B, which in combination can act synergistically. We compared the molecular interactions of the streptogramin combinations Synercid (type A, dalfopristin; type B, quinupristin) and NXL 103 (type A, flopristin; type B, linopristin) with the Escherichia coli 70S ribosome by X-ray crystallography. We further analyzed the activity of the streptogramin components individually and in combination. The streptogramin A and B components in Synercid and NXL 103 exhibit synergistic antimicrobial activity against certain pathogenic bacteria. However, in transcription-coupled translation assays, only combinations that include dalfopristin, the streptogramin A component of Synercid, show synergy. Notably, the diethylaminoethylsulfonyl group in dalfopristin reduces its activity but is the basis for synergy in transcription-coupled translation assays before its rapid hydrolysis from the depsipeptide core. Replacement of the diethylaminoethylsulfonyl group in dalfopristin by a nonhydrolyzable group may therefore be beneficial for synergy. The absence of general streptogramin synergy in transcription-coupled translation assays suggests that the synergistic antimicrobial activity of streptogramins can occur independently of the effects of streptogramin on translation.