+Open data
-Basic information
Entry | Database: PDB / ID: 6yj4 | |||||||||
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Title | Structure of Yarrowia lipolytica complex I at 2.7 A | |||||||||
Components |
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Keywords | MEMBRANE PROTEIN / NADH:Ubiquinone Oxidoreductase / complex I | |||||||||
Function / homology | Function and homology information lipoate biosynthetic process / NADH dehydrogenase / TIM23 mitochondrial import inner membrane translocase complex / mitochondrial [2Fe-2S] assembly complex / protein import into mitochondrial matrix / ubiquinone-6 biosynthetic process / respiratory chain complex I / cellular respiration / oxidoreductase activity, acting on NAD(P)H / iron-sulfur cluster assembly ...lipoate biosynthetic process / NADH dehydrogenase / TIM23 mitochondrial import inner membrane translocase complex / mitochondrial [2Fe-2S] assembly complex / protein import into mitochondrial matrix / ubiquinone-6 biosynthetic process / respiratory chain complex I / cellular respiration / oxidoreductase activity, acting on NAD(P)H / iron-sulfur cluster assembly / NADH dehydrogenase activity / NADH:ubiquinone reductase (H+-translocating) / acyl binding / ubiquinone binding / acyl carrier activity / quinone binding / electron transport coupled proton transport / : / ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / respiratory electron transport chain / : / mitochondrial electron transport, NADH to ubiquinone / NADH dehydrogenase (ubiquinone) activity / electron transport chain / mitochondrial membrane / aerobic respiration / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / oxidoreductase activity / mitochondrial inner membrane / protein-containing complex binding / mitochondrion / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Yarrowia lipolytica (yeast) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Hirst, J. / Grba, D. | |||||||||
Funding support | United Kingdom, 2items
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Citation | 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. #1: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6yj4.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6yj4.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 6yj4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yj4_validation.pdf.gz | 3.4 MB | Display | wwPDB validaton report |
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Full document | 6yj4_full_validation.pdf.gz | 3.5 MB | Display | |
Data in XML | 6yj4_validation.xml.gz | 231.9 KB | Display | |
Data in CIF | 6yj4_validation.cif.gz | 343.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/6yj4 ftp://data.pdbj.org/pub/pdb/validation_reports/yj/6yj4 | HTTPS FTP |
-Related structure data
Related structure data | 10815MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-NADH-ubiquinone oxidoreductase chain ... , 6 types, 6 molecules AHJKLM
#1: Protein | Mass: 14506.339 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nad3, YALI1_M00472r / Production host: Yarrowia lipolytica (yeast) References: UniProt: S5TMS4, UniProt: Q9B6C7*PLUS, NADH:ubiquinone reductase (H+-translocating) |
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#8: Protein | Mass: 38389.277 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nad1, YALI1_M00064g / Production host: Yarrowia lipolytica (yeast) References: UniProt: S5U3V2, UniProt: Q9B6E8*PLUS, NADH:ubiquinone reductase (H+-translocating) |
#10: Protein | Mass: 20793.111 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yarrowia lipolytica (strain CLIB 122 / E 150) (yeast) Gene: ND6 / Production host: Yarrowia lipolytica (yeast) References: UniProt: Q9B6E9, NADH:ubiquinone reductase (H+-translocating) |
#11: Protein | Mass: 9843.860 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nad4L, YALI1_M00335g / Production host: Yarrowia lipolytica (yeast) References: UniProt: S5U4U1, UniProt: Q9B6D4*PLUS, NADH:ubiquinone reductase (H+-translocating) |
#12: Protein | Mass: 73768.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nad5, YALI1_M00338r / Production host: Yarrowia lipolytica (yeast) References: UniProt: S5TF58, UniProt: Q9B6D3*PLUS, NADH:ubiquinone reductase (H+-translocating) |
#13: Protein | Mass: 54534.652 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nad4, YALI1_M00296g / Production host: Yarrowia lipolytica (yeast) References: UniProt: S5TMP9, UniProt: Q9B6D6*PLUS, NADH:ubiquinone reductase (H+-translocating) |
+Protein , 34 types, 34 molecules BCDEFGINOPQRSVWXYZabcdefghijkl...
-Acyl carrier protein ... , 2 types, 2 molecules TU
#20: Protein | Mass: 12053.585 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: YALI1_D18037g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6PXT9, UniProt: Q6C926*PLUS |
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#21: Protein | Mass: 14444.458 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: YALI1_D32594g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NG21, UniProt: Q6C7X2*PLUS |
-Sugars , 1 types, 5 molecules
#45: Sugar | ChemComp-LMT / |
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-Non-polymers , 10 types, 320 molecules
#43: Chemical | ChemComp-3PE / #44: Chemical | ChemComp-SF4 / #46: Chemical | ChemComp-PLC / #47: Chemical | #48: Chemical | ChemComp-FMN / | #49: Chemical | ChemComp-CDL / #50: Chemical | ChemComp-NDP / | #51: Chemical | ChemComp-ZN / | #52: Chemical | #53: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Source (recombinant) |
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Buffer solution | pH: 7.45 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Details: Gold grids pre-treated with PEG thiol reagent / Grid material: GOLD / Grid type: UltrAuFoil | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Calibrated defocus min: -1500 nm / Calibrated defocus max: -2700 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Image recording | Electron dose: 44 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2540 |
Image scans | Movie frames/image: 25 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 106302 / Details: Post manual curation of Relion auto-pick | ||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49669 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6G2J |