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	Plant-specific features of respiratory supercomplex I + III from Vigna radiata.
Journal, issue, pages	Nat Plants, Vol. 9, Issue 1, Page 157-168, Year 2023
Publish date	Dec 29, 2022
Authors	M Maldonado / Z Fan / K M Abe / J A Letts /
PubMed Abstract	The last steps of cellular respiration-an essential metabolic process in plants-are carried out by mitochondrial oxidative phosphorylation. This process involves a chain of multi-subunit membrane ...The last steps of cellular respiration-an essential metabolic process in plants-are carried out by mitochondrial oxidative phosphorylation. This process involves a chain of multi-subunit membrane protein complexes (complexes I-V) that form higher-order assemblies called supercomplexes. Although supercomplexes are the most physiologically relevant form of the oxidative phosphorylation complexes, their functions and structures remain mostly unknown. Here we present the cryogenic electron microscopy structure of the supercomplex I + III from Vigna radiata (mung bean). The structure contains the full subunit complement of complex I, including a newly assigned, plant-specific subunit. It also shows differences in the mitochondrial processing peptidase domain of complex III relative to a previously determined supercomplex with complex IV. The supercomplex interface, while reminiscent of that in other organisms, is plant specific, with a major interface involving complex III's mitochondrial processing peptidase domain and no participation of complex I's bridge domain. The complex I structure suggests that the bridge domain sets the angle between the enzyme's two arms, limiting large-scale conformational changes. Moreover, complex I's catalytic loops and its response in active-to-deactive assays suggest that, in V. radiata, the resting complex adopts a non-canonical state and can sample deactive- or open-like conformations even in the presence of substrate. This study widens our understanding of the possible conformations and behaviour of complex I and supercomplex I + III. Further studies of complex I and its supercomplexes in diverse organisms are needed to determine the universal and clade-specific mechanisms of respiration.
External links	Nat Plants / PubMed:36581760 / PubMed Central
Methods	EM (single particle)
Resolution	3.2 - 5.4 Å
Structure data	27934 8e73 EMDB-27934, PDB-8e73: Vigna radiata supercomplex I+III2 (full bridge) Method: EM (single particle) / Resolution: 3.2 Å EMDB-28798: Vigna radiata supercomplex I+III2 - bridgeless classes 1 Method: EM (single particle) / Resolution: 5.0 Å EMDB-28799: Vigna radiata respiratory complex I Method: EM (single particle) / Resolution: 3.8 Å EMDB-29088: Focused refinement of V. radiata respiratory supercomplex I+III2 around complex I bridge Method: EM (single particle) / Resolution: 3.2 Å EMDB-29089: Focused refinement of V. radiata respiratory supercomplex I+III2 around complex I heel Method: EM (single particle) / Resolution: 3.2 Å EMDB-29090: Focused refinement of V. radiata respiratory supercomplex I+III2 around complex I Pd domain Method: EM (single particle) / Resolution: 3.2 Å EMDB-29091: Focused refinement of V. radiata respiratory supercomplex I+III2 around complex III2 dimer Method: EM (single particle) / Resolution: 3.2 Å EMDB-29092: Focused refinement of V. radiata respiratory supercomplex I+III2 around complex I N module Method: EM (single particle) / Resolution: 3.2 Å EMDB-29093: Focused refinement of V. radiata respiratory supercomplex I+III2 around complex III2 proximal MPP domain Method: EM (single particle) / Resolution: 3.5 Å EMDB-29094: Focused refinement of V. radiata respiratory supercomplex I+III2 around complex III2 distal MPP domain Method: EM (single particle) / Resolution: 3.6 Å EMDB-29095: V. radiata respiratory supercomplex I+III2 bridged class 2 Method: EM (single particle) / Resolution: 3.6 Å EMDB-29190: V. radiata respiratory supercomplex I+III2 bridgeless class 3 Method: EM (single particle) / Resolution: 4.6 Å EMDB-29191: V. radiata respiratory supercomplex I+III2 bridgeless class 2 Method: EM (single particle) / Resolution: 5.4 Å EMDB-29203: V. radiata respiratory supercomplex I+III2 bridgeless class 4 Method: EM (single particle) / Resolution: 4.9 Å
Chemicals	ChemComp-PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipidYM / Phosphatidylcholine ChemComp-CDL: CARDIOLIPIN / phospholipidYM / Cardiolipin ChemComp-HEM: PROTOPORPHYRIN IX CONTAINING FE / Heme B ChemComp-3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipidYM / Phosphatidylethanolamine ChemComp-HEC: HEME C / Heme C ChemComp-U10: UBIQUINONE-10 / Coenzyme Q10 ChemComp-NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate ChemComp-ZMP: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate ChemComp-FE: Unknown entry / Iron ChemComp-ZN: Unknown entry ChemComp-SF4: IRON/SULFUR CLUSTER / Iron–sulfur cluster ChemComp-FES: FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster ChemComp-FMN*: FLAVIN MONONUCLEOTIDE / Flavin mononucleotide
Source	vigna radiata (mung bean)
Keywords	ELECTRON TRANSPORT / respiratory supercomplex / nadh-cyt c oxidoreductase / membrane complex