Journal: Nat Struct Mol Biol / Year: 2020 Title: Mitochondrial complex I structure reveals ordered water molecules for catalysis and proton translocation. Authors: Daniel N Grba / Judy Hirst / Abstract: Mitochondrial complex I powers ATP synthesis by oxidative phosphorylation, exploiting the energy from ubiquinone reduction by NADH to drive protons across the energy-transducing inner membrane. ...Mitochondrial complex I powers ATP synthesis by oxidative phosphorylation, exploiting the energy from ubiquinone reduction by NADH to drive protons across the energy-transducing inner membrane. Recent cryo-EM analyses of mammalian and yeast complex I have revolutionized structural and mechanistic knowledge and defined structures in different functional states. Here, we describe a 2.7-Å-resolution structure of the 42-subunit complex I from the yeast Yarrowia lipolytica containing 275 structured water molecules. We identify a proton-relay pathway for ubiquinone reduction and water molecules that connect mechanistically crucial elements and constitute proton-translocation pathways through the membrane. By comparison with known structures, we deconvolute structural changes governing the mammalian 'deactive transition' (relevant to ischemia-reperfusion injury) and their effects on the ubiquinone-binding site and a connected cavity in ND1. Our structure thus provides important insights into catalysis by this enigmatic respiratory machine.
History
Deposition
Apr 2, 2020
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Header (metadata) release
Aug 12, 2020
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Map release
Aug 12, 2020
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Update
Mar 17, 2021
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Current status
Mar 17, 2021
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2540 / Average electron dose: 44.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
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Image processing
Particle selection
Number selected: 106302 / Details: Post manual curation of Relion auto-pick
CTF correction
Software: (Name: RELION (ver. 3.1), Gctf)
Startup model
Type of model: EMDB MAP Details: Low-pass filtered (60 angstroms) in-house map from previous work
Initial angle assignment
Type: PROJECTION MATCHING / Software - Name: RELION (ver. 3.1) Details: Initial 2D classification to remove junk before the same in 3D classification.
Final 3D classification
Number classes: 2 / Avg.num./class: 50000 / Software - Name: RELION (ver. 3.1) / Details: One major good class isolated.
Final angle assignment
Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) / Details: Using Relion solvent-flattened 3D refinement
Final reconstruction
Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 49669
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Movie
Controller
Open data
Basic information
Map data
Sample
Function and homology information
NADH dehydrogenase / TIM23 mitochondrial import inner membrane translocase complex / mitochondrial iron-sulfur cluster assembly complex / protein import into mitochondrial matrix / ubiquinone-6 biosynthetic process / 
Authors
United Kingdom, 2 items 
Citation
Structure visualization
Downloads & links
emd_10815.png
http://ftp.pdbj.org/pub/emdb/structures/EMD-10815
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Y
X
Sample components
Processing
Electron microscopy
