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	HflX-mediated drug resistance through ribosome splitting and rRNA disordering in mycobacteria.
Journal, issue, pages	Proc Natl Acad Sci U S A, Vol. 122, Issue 6, Page e2419826122, Year 2025
Publish date	Feb 11, 2025
Authors	Soneya Majumdar / Amuliya Kashyap / Ravi K Koripella / Manjuli R Sharma / Kelley Hurst-Hess / Swati R Manjari / Nilesh K Banavali / Pallavi Ghosh / Rajendra K Agrawal /
PubMed Abstract	HflX is a highly conserved ribosome-associated GTPase implicated in rescuing stalled ribosomes and mediating antibiotic resistance in several bacteria, including macrolide-lincosamide antibiotic ...HflX is a highly conserved ribosome-associated GTPase implicated in rescuing stalled ribosomes and mediating antibiotic resistance in several bacteria, including macrolide-lincosamide antibiotic resistance in mycobacteria. Mycobacterial HflXs carry a distinct N-terminal extension (NTE) and a small insertion, as compared to their eubacterial homologs. Here, we present several high-resolution cryo-EM structures of mycobacterial HflX in complex with the 70S ribosome and its 50S subunit, with and without antibiotics. These structures reveal a distinct mechanism for HflX-mediated ribosome splitting and antibiotic resistance in mycobacteria. Our findings indicate that the NTE of mycobacterial HflX induces persistent disordering of multiple 23S rRNA helices, facilitating the dissociation of the 70S ribosome and generating an inactive pool of 50S subunits. During this process, HflX undergoes a large conformational change that stabilizes its NTE. Mycobacterial HflX also acts as an anti-association factor by binding to predissociated 50S subunits. Our structures show that a mycobacteria-specific insertion in HflX reaches far into the peptidyl transferase center (PTC), such that it would overlap with the ribosome-bound macrolide antibiotics. However, in the presence of antibiotics, this insertion retracts, adjusts around, and interacts with the antibiotic molecules. These results suggest that mycobacterial HflX is agnostic to antibiotic presence in the PTC. It mediates antibiotic resistance by splitting antibiotic-stalled 70S ribosomes and inactivating the resulting 50S subunits.
External links	Proc Natl Acad Sci U S A / PubMed:39913204 / PubMed Central
Methods	EM (single particle)
Resolution	2.63 - 4.96 Å
Structure data	43267 8vio EMDB-43267, PDB-8vio: Structure of Mycobacterium smegmatis HflX bound to a 70S ribosome Method: EM (single particle) / Resolution: 3.26 Å 43294 8vk0 EMDB-43294, PDB-8vk0: Structure of Mycobacterium smegmatis 50S ribosomal subunit bound to HflX:50S-HflX-A Method: EM (single particle) / Resolution: 3.14 Å 43305 8vk7 EMDB-43305, PDB-8vk7: Structure of Mycobacterium smegmatis 50S ribosomal subunit bound to HflX:50S-HflX-B Method: EM (single particle) / Resolution: 3.09 Å 43317 8vki EMDB-43317, PDB-8vki: Structure of Mycobacterium smegmatis 50S ribosomal subunit bound to HflX:50S-HflX-C Method: EM (single particle) / Resolution: 2.96 Å 43333 8vkw EMDB-43333, PDB-8vkw: Structure of Mycobacterium smegmatis 50S ribosomal subunit bound to delNTE-HflX Method: EM (single particle) / Resolution: 3.44 Å 43409 8vpk EMDB-43409, PDB-8vpk: Structure of Mycobacterium smegmatis 50S ribosomal subunit bound to HflX and erythromycin:50S-HflX-B-Ery Method: EM (single particle) / Resolution: 2.63 Å 43476 8vr4 EMDB-43476, PDB-8vr4: Structure of Mycobacterium smegmatis 50S ribosomal subunit bound to HflX and erythromycin:50S-HflX-A-Ery Method: EM (single particle) / Resolution: 2.8 Å 43477 8vr8 EMDB-43477, PDB-8vr8: Structure of Mycobacterium smegmatis 50S ribosomal subunit bound to HflX and chloramphenicol:50S-HflX-B-Clm Method: EM (single particle) / Resolution: 3.25 Å 43484 8vrl EMDB-43484, PDB-8vrl: Structure of Mycobacterium smegmatis 50S ribosomal subunit bound to HflX and chloramphenicol:50S-HflX-A-Clm Method: EM (single particle) / Resolution: 3.33 Å EMDB-43778: Structure of HflX mediated, inactive Mycobacterium smegmatis 50S ribosomal subunit Method: EM (single particle) / Resolution: 3.0 Å EMDB-43791: Mycobacterium smegmatis 70S ribosome bound to P-tRNA Method: EM (single particle) / Resolution: 3.06 Å EMDB-44044: Pre-dissociated Mycobacterium smegmatis 50S ribosomal subunit-HflX-GMPPCP complex Method: EM (single particle) / Resolution: 4.96 Å
Chemicals	ChemComp-GCP: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-PCP, energy-carrying molecule analogueYM ChemComp-ERY: ERYTHROMYCIN A / antibioticYM ChemComp-CLM: CHLORAMPHENICOL / antibiotic*YM
Source	mycolicibacterium smegmatis mc2 155 (bacteria)
Keywords	RIBOSOME / ribosome splitting / Mycobacterium smegmatis 70S / HflX / TRANSLATION / Mycobacterium smegmatis 50S / disordered 23S rRNA helices / erythromycin / chloramphenicol