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	High-Resolution Structural Proteomics of Mitochondria Using the 'Build and Retrieve' Methodology.
Journal, issue, pages	Mol Cell Proteomics, Vol. 22, Issue 12, Page 100666, Year 2023
Publish date	Oct 14, 2023
Authors	Zhemin Zhang / Marios L Tringides / Christopher E Morgan / Masaru Miyagi / Jason A Mears / Charles L Hoppel / Edward W Yu /
PubMed Abstract	The application of integrated systems biology to the field of structural biology is a promising new direction, although it is still in the infant stages of development. Here we report the use of ...The application of integrated systems biology to the field of structural biology is a promising new direction, although it is still in the infant stages of development. Here we report the use of single particle cryo-EM to identify multiple proteins from three enriched heterogeneous fractions prepared from human liver mitochondrial lysate. We simultaneously identify and solve high-resolution structures of nine essential mitochondrial enzymes with key metabolic functions, including fatty acid catabolism, reactive oxidative species clearance, and amino acid metabolism. Our methodology also identified multiple distinct members of the acyl-CoA dehydrogenase family. This work highlights the potential of cryo-EM to explore tissue proteomics at the atomic level.
External links	Mol Cell Proteomics / PubMed:37839702 / PubMed Central
Methods	EM (single particle)
Resolution	2.31 - 3.15 Å
Structure data	40463 8sgp EMDB-40463, PDB-8sgp: human liver mitochondrial Medium-chain specific acyl-CoA dehydrogenase Method: EM (single particle) / Resolution: 2.69 Å 40465 8sgr EMDB-40465, PDB-8sgr: human liver mitochondrial Isovaleryl-CoA dehydrogenase Method: EM (single particle) / Resolution: 2.84 Å 40466 8sgs EMDB-40466, PDB-8sgs: human liver mitochondrial Short-chain specific acyl-CoA dehydrogenase Method: EM (single particle) / Resolution: 3.15 Å 40469 8sgv EMDB-40469, PDB-8sgv: human liver mitochondrial Catalase Method: EM (single particle) / Resolution: 2.58 Å 40493 8shs EMDB-40493, PDB-8shs: human liver mitochondrial Aldehyde dehydrogenase ALDH2 Method: EM (single particle) / Resolution: 2.66 Å 40556 8sk6 EMDB-40556, PDB-8sk6: human liver mitochondrial Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase Method: EM (single particle) / Resolution: 2.96 Å 40558 8sk8 EMDB-40558, PDB-8sk8: human liver mitochondrial Glutamate dehydrogenase 1 Method: EM (single particle) / Resolution: 2.31 Å 40565 8skr EMDB-40565, PDB-8skr: human liver mitochondrial Aspartate aminotransferase Method: EM (single particle) / Resolution: 2.99 Å 40566 8sks EMDB-40566, PDB-8sks: human liver mitochondrial Superoxide dismutase [Mn] Method: EM (single particle) / Resolution: 2.91 Å
Chemicals	ChemComp-FAD: FLAVIN-ADENINE DINUCLEOTIDE / FADYM / Flavin adenine dinucleotide ChemComp-COA: COENZYME A / Coenzyme A ChemComp-HEM: PROTOPORPHYRIN IX CONTAINING FE / Heme B ChemComp-NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate ChemComp-PLP: PYRIDOXAL-5'-PHOSPHATE / Pyridoxal phosphate ChemComp-MN*: Unknown entry
Source	homo sapiens (human)
Keywords	OXIDOREDUCTASE / human / liver / mitochondrial / Medium-chain specific acyl-CoA dehydrogenase / Isovaleryl-CoA dehydrogenase / Short-chain specific acyl-CoA dehydrogenase / Catalase / Aldehyde dehydrogenase / ALDH2 / ISOMERASE / Delta(3 / 5)-Delta(2 / 4)-dienoyl-CoA isomerase / Glutamate dehydrogenase 1 / TRANSFERASE / Aspartate aminotransferase / Superoxide dismutase [Mn]