PDBsum entry 4peb

Ribosome

PDB id: 4peb

Contents

Protein chains

271 a.a.

209 a.a.

201 a.a.

177 a.a.

176 a.a.

149 a.a.

141 a.a.

142 a.a.

122 a.a.

143 a.a.

136 a.a.

120 a.a.

116 a.a.

114 a.a.

117 a.a.

103 a.a.

110 a.a.

93 a.a.

102 a.a.

94 a.a.

76 a.a.

77 a.a.

63 a.a.

58 a.a.

56 a.a.

50 a.a.

46 a.a.

64 a.a.

38 a.a.

191 a.a.

DNA/RNA

Ligands

MHW-THR-DBB-PRO-MHU-MHV-004-MHT

Metals

_MG ×199

_ZN

Waters ×666

Obsolete entry

PDB id:

4peb

Name:

Ribosome

Title:

Crystal structure of the e. Coli ribosome bound to quinupristin. This file contains the 50s subunit of the first 70s ribosome with quinupristin bound.

Structure:

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

Source:

Escherichia coli str. K-12 substr. Mds42. Organism_taxid: 1110693. Escherichia coli. Organism_taxid: 83333. Strain: k12. Thermus thermophilus. Organism_taxid: 300852. Strain: hb8 / atcc 27634 / dsm 579. Synthetic: yes.

Resolution:

2.95Å R-factor: 0.249 R-free: 0.282

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:

23-Apr-14 Release date: 30-Jul-14

Protein chain

P60422  (RL2_ECOLI) -  50S ribosomal protein L2 from Escherichia coli (strain K12)

Seq: 273 a.a.

Struc: 271 a.a.

Protein chain

P60438  (RL3_ECOLI) -  50S ribosomal protein L3 from Escherichia coli (strain K12)

Seq: 209 a.a.

Struc: 209 a.a.

Protein chain

P60723  (RL4_ECOLI) -  50S ribosomal protein L4 from Escherichia coli (strain K12)

Seq: 201 a.a.

Struc: 201 a.a.

Protein chain

P62399  (RL5_ECOLI) -  50S ribosomal protein L5 from Escherichia coli (strain K12)

Seq: 179 a.a.

Struc: 177 a.a.

Protein chain

P0AG55  (RL6_ECOLI) -  50S ribosomal protein L6 from Escherichia coli (strain K12)

Seq: 177 a.a.

Struc: 176 a.a.

Protein chain

P0A7R1  (RL9_ECOLI) -  50S ribosomal protein L9 from Escherichia coli (strain K12)

Seq: 149 a.a.

Struc: 149 a.a.

Protein chain

P0A7J7  (RL11_ECOLI) -  50S ribosomal protein L11 from Escherichia coli (strain K12)

Seq: 142 a.a.

Struc: 141 a.a.

Protein chain

P0AA10  (RL13_ECOLI) -  50S ribosomal protein L13 from Escherichia coli (strain K12)

Seq: 142 a.a.

Struc: 142 a.a.

Protein chain

P0ADY3  (RL14_ECOLI) -  50S ribosomal protein L14 from Escherichia coli (strain K12)

Seq: 123 a.a.

Struc: 122 a.a.

Protein chain

P02413  (RL15_ECOLI) -  50S ribosomal protein L15 from Escherichia coli (strain K12)

Seq: 144 a.a.

Struc: 143 a.a.

Protein chain

P0ADY7  (RL16_ECOLI) -  50S ribosomal protein L16 from Escherichia coli (strain K12)

Seq: 136 a.a.

Struc: 136 a.a.

Protein chain

P0AG44  (RL17_ECOLI) -  50S ribosomal protein L17 from Escherichia coli (strain K12)

Seq: 127 a.a.

Struc: 120 a.a.

Protein chain

P0C018  (RL18_ECOLI) -  50S ribosomal protein L18 from Escherichia coli (strain K12)

Seq: 117 a.a.

Struc: 116 a.a.

Protein chain

P0A7K6  (RL19_ECOLI) -  50S ribosomal protein L19 from Escherichia coli (strain K12)

Seq: 115 a.a.

Struc: 114 a.a.

Protein chain

P0A7L3  (RL20_ECOLI) -  50S ribosomal protein L20 from Escherichia coli (strain K12)

Seq: 118 a.a.

Struc: 117 a.a.

Protein chain

P0AG48  (RL21_ECOLI) -  50S ribosomal protein L21 from Escherichia coli (strain K12)

Seq: 103 a.a.

Struc: 103 a.a.

Protein chain

P61175  (RL22_ECOLI) -  50S ribosomal protein L22 from Escherichia coli (strain K12)

Seq: 110 a.a.

Struc: 110 a.a.

Protein chain

P0ADZ0  (RL23_ECOLI) -  50S ribosomal protein L23 from Escherichia coli (strain K12)

Seq: 100 a.a.

Struc: 93 a.a.

Protein chain

P60624  (RL24_ECOLI) -  50S ribosomal protein L24 from Escherichia coli (strain K12)

Seq: 104 a.a.

Struc: 102 a.a.

Protein chain

P68919  (RL25_ECOLI) -  50S ribosomal protein L25 from Escherichia coli (strain K12)

Seq: 94 a.a.

Struc: 94 a.a.

Protein chain

P0A7L8  (RL27_ECOLI) -  50S ribosomal protein L27 from Escherichia coli (strain K12)

Seq: 85 a.a.

Struc: 76 a.a.

Protein chain

P0A7M2  (RL28_ECOLI) -  50S ribosomal protein L28 from Escherichia coli (strain K12)

Seq: 78 a.a.

Struc: 77 a.a.

Protein chain

P0A7M6  (RL29_ECOLI) -  50S ribosomal protein L29 from Escherichia coli (strain K12)

Seq: 63 a.a.

Struc: 63 a.a.

Protein chain

P0AG51  (RL30_ECOLI) -  50S ribosomal protein L30 from Escherichia coli (strain K12)

Seq: 59 a.a.

Struc: 58 a.a.

Protein chain

P0A7N4  (RL32_ECOLI) -  50S ribosomal protein L32 from Escherichia coli (strain K12)

Seq: 57 a.a.

Struc: 56 a.a.

Protein chain

P0A7N9  (RL33_ECOLI) -  50S ribosomal protein L33 from Escherichia coli (strain K12)

Seq: 55 a.a.

Struc: 50 a.a.

Protein chain

P0A7P5  (RL34_ECOLI) -  50S ribosomal protein L34 from Escherichia coli (strain K12)

Seq: 46 a.a.

Struc: 46 a.a.

Protein chain

P0A7Q1  (RL35_ECOLI) -  50S ribosomal protein L35 from Escherichia coli (strain K12)

Seq: 65 a.a.

Struc: 64 a.a.

Protein chain

P0A7Q6  (RL36_ECOLI) -  50S ribosomal protein L36 from Escherichia coli (strain K12)

Seq: 38 a.a.

Struc: 38 a.a.

Protein chain

Q5SLP7  (RL1_THET8) -  50S ribosomal protein L1 from Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

Seq: 229 a.a.

Struc: 191 a.a.

DNA/RNA chains

G-G-U-U-A-A-G-C-G-A-C-U-A-A-G-C-G-U-A-C-A-C-G-G-U-G-G-A-U-G-C-C-C-U-G-G-C-A-G- ... 2897 bases

U-G-C-C-U-G-G-C-G-G-C-C-G-U-A-G-C-G-C-G-G-U-G-G-U-C-C-C-A-C-C-U-G-A-C-C-C-C-A- 119 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.