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	Key role of quinone in the mechanism of respiratory complex I.
Journal, issue, pages	Nat Commun, Vol. 11, Issue 1, Page 4135, Year 2020
Publish date	Aug 18, 2020
Authors	Javier Gutiérrez-Fernández / Karol Kaszuba / Gurdeep S Minhas / Rozbeh Baradaran / Margherita Tambalo / David T Gallagher / Leonid A Sazanov /
PubMed Abstract	Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in ...Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in complex I is not known. Here we report five crystal structures of T. thermophilus enzyme in complex with NADH or quinone-like compounds. We also determined cryo-EM structures of major and minor native states of the complex, differing in the position of the peripheral arm. Crystal structures show that binding of quinone-like compounds (but not of NADH) leads to a related global conformational change, accompanied by local re-arrangements propagating from the quinone site to the nearest proton channel. Normal mode and molecular dynamics analyses indicate that these are likely to represent the first steps in the proton translocation mechanism. Our results suggest that quinone binding and chemistry play a key role in the coupling mechanism of complex I.
External links	Nat Commun / PubMed:32811817 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	3.109 - 6.1 Å
Structure data	11231 6ziy EMDB-11231, PDB-6ziy: Respiratory complex I from Thermus thermophilus, NADH dataset, major state Method: EM (single particle) / Resolution: 4.25 Å 11235 6zjl EMDB-11235, PDB-6zjl: Respiratory complex I from Thermus thermophilus, NAD+ dataset, major state Method: EM (single particle) / Resolution: 4.3 Å 11237 6zjn EMDB-11237, PDB-6zjn: Respiratory complex I from Thermus thermophilus, NADH dataset, minor state Method: EM (single particle) / Resolution: 6.1 Å 11238 6zjy EMDB-11238, PDB-6zjy: Respiratory complex I from Thermus thermophilus, NAD+ dataset, minor state Method: EM (single particle) / Resolution: 5.5 Å PDB-6i0d: Respiratory complex I from Thermus thermophilus with bound Decyl-Ubiquinone Method: X-RAY DIFFRACTION / Resolution: 3.6 Å PDB-6i1p: Respiratory complex I from Thermus thermophilus with bound NADH Method: X-RAY DIFFRACTION / Resolution: 3.207 Å PDB-6q8o: Respiratory complex I from Thermus thermophilus with bound Piericidin A Method: X-RAY DIFFRACTION / Resolution: 3.605 Å PDB-6q8w: Respiratory complex I from Thermus thermophilus with bound Aureothin. Method: X-RAY DIFFRACTION / Resolution: 3.4 Å PDB-6q8x: Respiratory complex I from Thermus thermophilus with bound Pyridaben. Method: X-RAY DIFFRACTION / Resolution: 3.508 Å PDB-6y11: Respiratory complex I from Thermus thermophilus Method: X-RAY DIFFRACTION / Resolution: 3.109 Å
Chemicals	ChemComp-SF4: IRON/SULFUR CLUSTER ChemComp-FMN: FLAVIN MONONUCLEOTIDE ChemComp-FES: FE2/S2 (INORGANIC) CLUSTER ChemComp-DCQ: 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione ChemComp-NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE ChemComp-HQH: Piericidin A / antibioticYM ChemComp-HQW: Aureothin / antitumor, antifungal, antibioticYM ChemComp-HQK: Pyridaben
Source	thermus thermophilus (bacteria) thermus thermophilus hb8 (bacteria) thermus thermophilus (strain hb8 / atcc 27634 / dsm 579) (bacteria)
Keywords	MEMBRANE PROTEIN / Respiratory chain / complex I / NADH:ubiquinone oxidoreductase / electron transfer / proton translocation