4V7U

Crystal structure of the E. coli ribosome bound to erythromycin.

This is a non-PDB format compatible entry.

Summary for 4V7U

• Entry DOI: 10.2210/pdb4v7u/pdb
• Related: 3OAQ 3OAR 3OAS 3OAT 3OFA 3OFB 3OFC 3OFD 3OFP 3OFQ 3OFR 3OFX 3OFY 3OFZ 3OG0
• Descriptor: 16S rRNA, 30S ribosomal protein S10, 30S ribosomal protein S11, ... (56 entities in total)
• Functional Keywords: protein biosynthesis, ribosomes, rna, trna, transfer, erythromycin, ketolide, macrolide, antibiotic, exit, peptidyl, 30s, 70s, 16s, ribosomal subunit, small, ribosome
• Biological source: Escherichia coli; More
• Total number of polymer chains: 104
• Total formula weight: 4237520.46

Authors

Dunkle, J.A.,Xiong, L.,Mankin, A.S.,Cate, J.H.D. (deposition date: 2010-08-15, release date: 2014-07-09, Last modification date: 2024-11-20)

Primary citation

Dunkle, J.A.,Xiong, L.,Mankin, A.S.,Cate, J.H.
Structures of the Escherichia coli ribosome with antibiotics bound near the peptidyl transferase center explain spectra of drug action.
Proc.Natl.Acad.Sci.USA, 107:17152-17157, 2010

PubMed Abstract: Differences between the structures of bacterial, archaeal, and eukaryotic ribosomes account for the selective action of antibiotics. Even minor variations in the structure of ribosomes of different bacterial species may lead to idiosyncratic, species-specific interactions of the drugs with their targets. Although crystallographic structures of antibiotics bound to the peptidyl transferase center or the exit tunnel of archaeal (Haloarcula marismortui) and bacterial (Deinococcus radiodurans) large ribosomal subunits have been reported, it remains unclear whether the interactions of antibiotics with these ribosomes accurately reflect those with the ribosomes of pathogenic bacteria. Here we report X-ray crystal structures of the Escherichia coli ribosome in complexes with clinically important antibiotics of four major classes, including the macrolide erythromycin, the ketolide telithromycin, the lincosamide clindamycin, and a phenicol, chloramphenicol, at resolutions of ∼3.3 Å-3.4 Å. Binding modes of three of these antibiotics show important variations compared to the previously determined structures. Biochemical and structural evidence also indicates that interactions of telithromycin with the E. coli ribosome more closely resembles drug binding to ribosomes of bacterial pathogens. The present data further argue that the identity of nucleotides 752, 2609, and 2055 of 23S ribosomal RNA explain in part the spectrum and selectivity of antibiotic action.

PubMed: 20876128
DOI: 10.1073/pnas.1007988107

Experimental method

X-RAY DIFFRACTION (3.1 Å)