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 mitoribosomal small subunit biogenesis and preinitiation.
Journal, issue, pages	Nature, Vol. 606, Issue 7914, Page 603-608, Year 2022
Publish date	Jun 8, 2022
Authors	Yuzuru Itoh / Anas Khawaja / Ivan Laptev / Miriam Cipullo / Ilian Atanassov / Petr Sergiev / Joanna Rorbach / Alexey Amunts /
PubMed Abstract	Mitoribosomes are essential for the synthesis and maintenance of bioenergetic proteins. Here we use cryo-electron microscopy to determine a series of the small mitoribosomal subunit (SSU) ...Mitoribosomes are essential for the synthesis and maintenance of bioenergetic proteins. Here we use cryo-electron microscopy to determine a series of the small mitoribosomal subunit (SSU) intermediates in complex with auxiliary factors, revealing a sequential assembly mechanism. The methyltransferase TFB1M binds to partially unfolded rRNA h45 that is promoted by RBFA, while the mRNA channel is blocked. This enables binding of METTL15 that promotes further rRNA maturation and a large conformational change of RBFA. The new conformation allows initiation factor mtIF3 to already occupy the subunit interface during the assembly. Finally, the mitochondria-specific ribosomal protein mS37 (ref. ) outcompetes RBFA to complete the assembly with the SSU-mS37-mtIF3 complex that proceeds towards mtIF2 binding and translation initiation. Our results explain how the action of step-specific factors modulate the dynamic assembly of the SSU, and adaptation of a unique protein, mS37, links the assembly to initiation to establish the catalytic human mitoribosome.
External links	Nature / PubMed:35676484 / PubMed Central
Methods	EM (single particle)
Resolution	2.56 - 3.19 Å
Structure data	13551 7pnt EMDB-13551, PDB-7pnt: Assembly intermediate of mouse mitochondrial ribosome small subunit without mS37 in complex with RbfA and Tfb1m Method: EM (single particle) / Resolution: 3.19 Å 13552 7pnu EMDB-13552, PDB-7pnu: Assembly intermediate of mouse mitochondrial ribosome small subunit without mS37 in complex with RbfA inward conformation Method: EM (single particle) / Resolution: 3.06 Å 13553 7pnv EMDB-13553, PDB-7pnv: Assembly intermediate of mouse mitochondrial ribosome small subunit without mS37 in complex with RbfA and Mettl15 Method: EM (single particle) / Resolution: 3.06 Å 13554 7pnw EMDB-13554, PDB-7pnw: Mouse mitochondrial ribosome small subunit lacking m5U modification Method: EM (single particle) / Resolution: 3.09 Å 13555 7pnx EMDB-13555, PDB-7pnx: Assembly intermediate of human mitochondrial ribosome small subunit without mS37 in complex with RBFA and METTL15 conformation a Method: EM (single particle) / Resolution: 2.76 Å 13556 7pny EMDB-13556, PDB-7pny: Assembly intermediate of human mitochondrial ribosome small subunit without mS37 in complex with RBFA and METTL15 conformation b Method: EM (single particle) / Resolution: 3.06 Å 13557 7pnz EMDB-13557, PDB-7pnz: Assembly intermediate of human mitochondrial ribosome small subunit without mS37 in complex with RBFA and METTL15 conformation c Method: EM (single particle) / Resolution: 3.09 Å 13558 7po0 EMDB-13558, PDB-7po0: Assembly intermediate of human mitochondrial ribosome small subunit without mS37 in complex with RBFA and IF3 Method: EM (single particle) / Resolution: 2.9 Å 13559 7po1 EMDB-13559, PDB-7po1: Initiation complex of human mitochondrial ribosome small subunit with IF3 Method: EM (single particle) / Resolution: 2.92 Å 13560 7po2 EMDB-13560, PDB-7po2: Initiation complex of human mitochondrial ribosome small subunit with IF2, fMet-tRNAMet and mRNA Method: EM (single particle) / Resolution: 3.09 Å 13561 7po3 EMDB-13561, PDB-7po3: Human mitochondrial ribosome small subunit Method: EM (single particle) / Resolution: 2.92 Å 13562 7po4 EMDB-13562, PDB-7po4: Assembly intermediate of human mitochondrial ribosome large subunit (largely unfolded rRNA with MALSU1, L0R8F8 and ACP) Method: EM (single particle) / Resolution: 2.56 Å
Chemicals	ChemComp-MG: Unknown entry ChemComp-K: Unknown entry ChemComp-ZN: Unknown entry ChemComp-FES: FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying moleculeYM / Adenosine triphosphate ChemComp-HOH: WATER / Water ChemComp-SAH: S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine ChemComp-NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NADYM / Nicotinamide adenine dinucleotide ChemComp-GDP: GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying moleculeYM / Guanosine diphosphate ChemComp-FME: N-FORMYLMETHIONINE / N-Formylmethionine ChemComp-GTP: GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying moleculeYM / Guanosine triphosphate ChemComp-8Q1: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate
Source	mus musculus (house mouse) homo sapiens (human)
Keywords	RIBOSOME / Assembly intermediate / maturation / biogenesis / small subunit / mitochondrion / Initiation factor 3 / translation