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	Mechanism of 5S RNP recruitment and helicase-surveilled rRNA maturation during pre-60S biogenesis.
Journal, issue, pages	EMBO Rep, Vol. 24, Issue 7, Page e56910, Year 2023
Publish date	Jul 5, 2023
Authors	Benjamin Lau / Zixuan Huang / Nikola Kellner / Shuangshuang Niu / Otto Berninghausen / Roland Beckmann / Ed Hurt / Jingdong Cheng /
PubMed Abstract	Ribosome biogenesis proceeds along a multifaceted pathway from the nucleolus to the cytoplasm that is extensively coupled to several quality control mechanisms. However, the mode by which 5S ...Ribosome biogenesis proceeds along a multifaceted pathway from the nucleolus to the cytoplasm that is extensively coupled to several quality control mechanisms. However, the mode by which 5S ribosomal RNA is incorporated into the developing pre-60S ribosome, which in humans links ribosome biogenesis to cell proliferation by surveillance by factors such as p53-MDM2, is poorly understood. Here, we report nine nucleolar pre-60S cryo-EM structures from Chaetomium thermophilum, one of which clarifies the mechanism of 5S RNP incorporation into the early pre-60S. Successive assembly states then represent how helicases Dbp10 and Spb4, and the Pumilio domain factor Puf6 act in series to surveil the gradual folding of the nearby 25S rRNA domain IV. Finally, the methyltransferase Spb1 methylates a universally conserved guanine nucleotide in the A-loop of the peptidyl transferase center, thereby licensing further maturation. Our findings provide insight into the hierarchical action of helicases in safeguarding rRNA tertiary structure folding and coupling to surveillance mechanisms that culminate in local RNA modification.
External links	EMBO Rep / PubMed:37129998 / PubMed Central
Methods	EM (single particle)
Resolution	2.7 - 3.6 Å
Structure data	35279 8i9p EMDB-35279, PDB-8i9p: Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Mak16 Method: EM (single particle) / Resolution: 3.0 Å 35281 8i9r EMDB-35281, PDB-8i9r: Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State 5S RNP Method: EM (single particle) / Resolution: 3.1 Å 35283 8i9t EMDB-35283, PDB-8i9t: Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Dbp10-1 Method: EM (single particle) / Resolution: 3.6 Å 35285 8i9v EMDB-35285, PDB-8i9v: Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Dbp10-2 Method: EM (single particle) / Resolution: 3.1 Å 35286 8i9w EMDB-35286, PDB-8i9w: Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - Dbp10-3 Method: EM (single particle) / Resolution: 3.1 Å 35287 8i9x EMDB-35287, PDB-8i9x: Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - Ytm1-1 Method: EM (single particle) / Resolution: 2.8 Å 35288 8i9y EMDB-35288, PDB-8i9y: Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - Ytm1-2 Method: EM (single particle) / Resolution: 3.1 Å 35289 8i9z EMDB-35289, PDB-8i9z: Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Spb4 Method: EM (single particle) / Resolution: 2.7 Å 35290 8ia0 EMDB-35290, PDB-8ia0: Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Puf6 Method: EM (single particle) / Resolution: 2.7 Å
Chemicals	ChemComp-ZN: Unknown entry ChemComp-GTP: GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying moleculeYM / Guanosine triphosphate ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM / Adenosine diphosphate ChemComp-MG: Unknown entry
Source	chaetomium thermophilum (fungus)
Keywords	RIBOSOME / Ribosome biogenesis / pre-60S ribosome