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	Molecular basis for recognition and deubiquitination of 40S ribosomes by Otu2.
Journal, issue, pages	Nat Commun, Vol. 14, Issue 1, Page 2730, Year 2023
Publish date	May 12, 2023
Authors	Ken Ikeuchi / Nives Ivic / Robert Buschauer / Jingdong Cheng / Thomas Fröhlich / Yoshitaka Matsuo / Otto Berninghausen / Toshifumi Inada / Thomas Becker / Roland Beckmann /
PubMed Abstract	In actively translating 80S ribosomes the ribosomal protein eS7 of the 40S subunit is monoubiquitinated by the E3 ligase Not4 and deubiquitinated by Otu2 upon ribosomal subunit recycling. Despite its ...In actively translating 80S ribosomes the ribosomal protein eS7 of the 40S subunit is monoubiquitinated by the E3 ligase Not4 and deubiquitinated by Otu2 upon ribosomal subunit recycling. Despite its importance for translation efficiency the exact role and structural basis for this translational reset is poorly understood. Here, structural analysis by cryo-electron microscopy of native and reconstituted Otu2-bound ribosomal complexes reveals that Otu2 engages 40S subunits mainly between ribosome recycling and initiation stages. Otu2 binds to several sites on the intersubunit surface of the 40S that are not occupied by any other 40S-binding factors. This binding mode explains the discrimination against 80S ribosomes via the largely helical N-terminal domain of Otu2 as well as the specificity for mono-ubiquitinated eS7 on 40S. Collectively, this study reveals mechanistic insights into the Otu2-driven deubiquitination steps for translational reset during ribosome recycling/(re)initiation.
External links	Nat Commun / PubMed:37169754 / PubMed Central
Methods	EM (single particle)
Resolution	2.9 - 3.8 Å
Structure data	16470 8c83 EMDB-16470: Cryo-EM structure of in vitro reconstituted Otu2-bound Ub-40S complex - body 1 PDB-8c83: Cryo-EM structure of in vitro reconstituted Otu2-bound Ub-40S complex Method: EM (single particle) / Resolution: 3.0 Å EMDB-16471: in vitro reconstituted yeast 40S ribosome complex with deubiquitinating enzyme Otu2 bound to ubiquitinated eS7 - body 2 (40S head) Method: EM (single particle) / Resolution: 3.2 Å 16525 8cah EMDB-16525, PDB-8cah: Cryo-EM structure of native Otu2-bound ubiquitinated 43S pre-initiation complex Method: EM (single particle) / Resolution: 3.0 Å 16533 8cas EMDB-16533, PDB-8cas: Cryo-EM structure of native Otu2-bound ubiquitinated 48S initiation complex (partial) Method: EM (single particle) / Resolution: 3.3 Å 16541 8cbj EMDB-16541: Yeast cytoplasmic pre-40S ribosome biogenesis complex with deubiquitinating enzyme Otu2 PDB-8cbj: Cryo-EM structure of Otu2-bound cytoplasmic pre-40S ribosome biogenesis complex Method: EM (single particle) / Resolution: 3.8 Å EMDB-16542: Local refinement map of Otu2 N-terminal domain bound to yeast 40S ribosome Method: EM (single particle) / Resolution: 2.9 Å EMDB-16548: Local refinement map of Otu2 C-terminal domain bound to ubiquitinated eS7 on yeast 40S ribosome Method: EM (single particle) / Resolution: 3.0 Å
Chemicals	ChemComp-MG: Unknown entry ChemComp-ZN: Unknown entry ChemComp-SF4: IRON/SULFUR CLUSTER / Iron–sulfur cluster ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM / Adenosine diphosphate ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying moleculeYM / Adenosine triphosphate ChemComp-MET: METHIONINE / Methionine ChemComp-GCP: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-PCP, energy-carrying molecule analogue*YM
Source	saccharomyces cerevisiae (brewer's yeast) baker's yeast (brewer's yeast) saccharomyces cerevisiae w303 (yeast)
Keywords	RIBOSOME / 40S / Ubiquitin / Deubiquitinating enzyme / Otu2 / Rps7 / Translation / Initiation / Complex / Biogenesis