Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Bactericidal effect of tetracycline in E. coli strain ED1a may be associated with ribosome dysfunction.
Journal, issue, pages	Nat Commun, Vol. 15, Issue 1, Page 4783, Year 2024
Publish date	Jun 5, 2024
Authors	Iskander Khusainov / Natalie Romanov / Camille Goemans / Beata Turoňová / Christian E Zimmerli / Sonja Welsch / Julian D Langer / Athanasios Typas / Martin Beck /
PubMed Abstract	Ribosomes translate the genetic code into proteins. Recent technical advances have facilitated in situ structural analyses of ribosome functional states inside eukaryotic cells and the minimal ...Ribosomes translate the genetic code into proteins. Recent technical advances have facilitated in situ structural analyses of ribosome functional states inside eukaryotic cells and the minimal bacterium Mycoplasma. However, such analyses of Gram-negative bacteria are lacking, despite their ribosomes being major antimicrobial drug targets. Here we compare two E. coli strains, a lab E. coli K-12 and human gut isolate E. coli ED1a, for which tetracycline exhibits bacteriostatic and bactericidal action, respectively. Using our approach for close-to-native E. coli sample preparation, we assess the two strains by cryo-ET and visualize their ribosomes at high resolution in situ. Upon tetracycline treatment, these exhibit virtually identical drug binding sites, yet the conformation distribution of ribosomal complexes differs. While K-12 retains ribosomes in a translation-competent state, tRNAs are lost in the vast majority of ED1a ribosomes. These structural findings together with the proteome-wide abundance and thermal stability assessments indicate that antibiotic responses are complex in cells and can differ between different strains of a single species, thus arguing that all relevant bacterial strains should be analyzed in situ when addressing antibiotic mode of action.
External links	Nat Commun / PubMed:38839776 / PubMed Central
Methods	EM (subtomogram averaging) / EM (single particle)
Resolution	2.75 - 8.5 Å
Structure data	EMDB-18036: In situ structure of E. coli 70S ribosome Method: EM (subtomogram averaging) / Resolution: 5.3 Å EMDB-18037: In situ 70S ribosome of E. coli K-12 untreated cells Method: EM (subtomogram averaging) / Resolution: 8.5 Å EMDB-18038: In situ 70S ribosome of E. coli K-12 cells treated with tetracycline Method: EM (subtomogram averaging) / Resolution: 8.5 Å EMDB-18039: In situ 70S ribosome of E. coli ED1a untreated cells Method: EM (subtomogram averaging) / Resolution: 7.5 Å EMDB-18040: In situ 70S ribosome of E. coli ED1a cells treated with tetracycline Method: EM (subtomogram averaging) / Resolution: 7.0 Å EMDB-18041: E. coli K-12 70S ribosome bound to mRNA A-tRNA, P-tRNA, E-tRNA Method: EM (single particle) / Resolution: 3.02 Å EMDB-18042: E. coli ED1a 70S ribosome bound to mRNA A-tRNA, P-tRNA, E-tRNA Method: EM (single particle) / Resolution: 3.02 Å EMDB-19206: E. coli ED1a 70S-tetracycline complex - focused refinement on 30S head Method: EM (single particle) / Resolution: 2.83 Å EMDB-19207: E. coli ED1a 70S-tetracycline complex - focused refinement on 30S body Method: EM (single particle) / Resolution: 2.83 Å EMDB-19208: E. coli ED1a 70S-tetracycline complex - focused refinement on 50S Method: EM (single particle) / Resolution: 2.75 Å
Source	Escherichia coli BW25113 (bacteria) Escherichia coli ED1a Escherichia coli BW