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	Cryo- EM structure of the mycobacterial 70S ribosome in complex with ribosome hibernation promotion factor RafH.
Journal, issue, pages	Nat Commun, Vol. 15, Issue 1, Page 638, Year 2024
Publish date	Jan 20, 2024
Authors	Niraj Kumar / Shivani Sharma / Prem S Kaushal /
PubMed Abstract	Ribosome hibernation is a key survival strategy bacteria adopt under environmental stress, where a protein, hibernation promotion factor (HPF), transitorily inactivates the ribosome. Mycobacterium ...Ribosome hibernation is a key survival strategy bacteria adopt under environmental stress, where a protein, hibernation promotion factor (HPF), transitorily inactivates the ribosome. Mycobacterium tuberculosis encounters hypoxia (low oxygen) as a major stress in the host macrophages, and upregulates the expression of RafH protein, which is crucial for its survival. The RafH, a dual domain HPF, an orthologue of bacterial long HPF (HPF), hibernates ribosome in 70S monosome form, whereas in other bacteria, the HPF induces 70S ribosome dimerization and hibernates its ribosome in 100S disome form. Here, we report the cryo- EM structure of M. smegmatis, a close homolog of M. tuberculosis, 70S ribosome in complex with the RafH factor at an overall 2.8 Å resolution. The N- terminus domain (NTD) of RafH binds to the decoding center, similarly to HPF NTD. In contrast, the C- terminus domain (CTD) of RafH, which is larger than the HPF CTD, binds to a distinct site at the platform binding center of the ribosomal small subunit. The two domain-connecting linker regions, which remain mostly disordered in earlier reported HPF structures, interact mainly with the anti-Shine Dalgarno sequence of the 16S rRNA.
External links	Nat Commun / PubMed:38245551 / PubMed Central
Methods	EM (single particle)
Resolution	2.7 - 3.5 Å
Structure data	37551 8whx EMDB-37551, PDB-8whx: Cryo- EM structure of Mycobacterium smegmatis 70S ribosome and RafH. Method: EM (single particle) / Resolution: 2.8 Å 37552 8why EMDB-37552, PDB-8why: Cryo- EM structure of Mycobacterium smegmatis 50S ribosomal subunit (body 1) of 70S ribosome and RafH. Method: EM (single particle) / Resolution: 2.7 Å 37559 8wi7 EMDB-37559, PDB-8wi7: Cryo- EM structure of Mycobacterium smegmatis 70S ribosome, bS1 and RafH. Method: EM (single particle) / Resolution: 3.5 Å 37560 8wi8 EMDB-37560, PDB-8wi8: Cryo- EM structure of Mycobacterium smegmatis 50S ribosomal subunit (body 1) of 70S ribosome, bS1 and RafH. Method: EM (single particle) / Resolution: 2.7 Å 37561 8wi9 EMDB-37561, PDB-8wi9: Cryo- EM structure of Mycobacterium smegmatis 30S ribosomal subunit (body 2) of 70S ribosome, bS1 and RafH. Method: EM (single particle) / Resolution: 3.5 Å 37562 8wib EMDB-37562, PDB-8wib: Cryo- EM structure of Mycobacterium smegmatis 70S ribosome, E- tRNA and RafH. Method: EM (single particle) / Resolution: 3.5 Å 37563 8wic EMDB-37563, PDB-8wic: Cryo- EM structure of Mycobacterium smegmatis 50S ribosomal subunit (body 1) of 70S ribosome, E- tRNA and RafH. Method: EM (single particle) / Resolution: 3.5 Å 37564 8wid EMDB-37564, PDB-8wid: Cryo- EM structure of Mycobacterium smegmatis 30S ribosomal subunit (body 2) of 70S ribosome, E- tRNA and RafH. Method: EM (single particle) / Resolution: 3.5 Å 37565 8wif EMDB-37565, PDB-8wif: Cryo- EM structure of Mycobacterium smegmatis 30S ribosomal subunit (body 2) of 70S ribosome and RafH. Method: EM (single particle) / Resolution: 2.9 Å
Source	mycolicibacterium smegmatis mc2 155 (bacteria)
Keywords	RIBOSOME / protein synthesis / Mycobacterium smegmatis / hibernation promotion factor / HPF / RafH / hypoxia stress / Cryo- EM / Single particle reconstruction / Single particle reconstruction.