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- PDB-8esw: Structure of mitochondrial complex I from Drosophila melanogaster... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8esw | ||||||
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Title | Structure of mitochondrial complex I from Drosophila melanogaster, Flexible-class 1 | ||||||
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![]() | OXIDOREDUCTASE / NADH:ubiquinone oxidoreductase / TRANSLOCASE | ||||||
Function / homology | ![]() Mitochondrial protein import / Glyoxylate metabolism and glycine degradation / Respiratory electron transport / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / RHOG GTPase cycle / NADH dehydrogenase / Mitochondrial protein degradation / regulation of terminal button organization / Neutrophil degranulation ...Mitochondrial protein import / Glyoxylate metabolism and glycine degradation / Respiratory electron transport / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / RHOG GTPase cycle / NADH dehydrogenase / Mitochondrial protein degradation / regulation of terminal button organization / Neutrophil degranulation / protein lipoylation / deoxynucleoside kinase activity / cellular respiration / ubiquinone-6 biosynthetic process / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / mitochondrial ATP synthesis coupled electron transport / : / mitochondrial electron transport, NADH to ubiquinone / : / mitochondrial respiratory chain complex I assembly / acyl binding / NADH dehydrogenase (ubiquinone) activity / acyl carrier activity / quinone binding / electron transport coupled proton transport / ATP synthesis coupled electron transport / aerobic respiration / respiratory electron transport chain / reactive oxygen species metabolic process / determination of adult lifespan / response to reactive oxygen species / mitochondrial membrane / mitochondrial intermembrane space / transmembrane transport / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / oxidoreductase activity / mitochondrial matrix / protein-containing complex binding / mitochondrion / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
![]() | Padavannil, A. / Letts, J.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Resting mitochondrial complex I from adopts a helix-locked state. Authors: Abhilash Padavannil / Anjaneyulu Murari / Shauna-Kay Rhooms / Edward Owusu-Ansah / James A Letts / ![]() Abstract: Respiratory complex I is a proton-pumping oxidoreductase key to bioenergetic metabolism. Biochemical studies have found a divide in the behavior of complex I in metazoans that aligns with the ...Respiratory complex I is a proton-pumping oxidoreductase key to bioenergetic metabolism. Biochemical studies have found a divide in the behavior of complex I in metazoans that aligns with the evolutionary split between Protostomia and Deuterostomia. Complex I from Deuterostomia including mammals can adopt a biochemically defined off-pathway 'deactive' state, whereas complex I from Protostomia cannot. The presence of off-pathway states complicates the interpretation of structural results and has led to considerable mechanistic debate. Here, we report the structure of mitochondrial complex I from the thoracic muscles of the model protostome . We show that although complex I (-CI) does not have a NEM-sensitive deactive state, it does show slow activation kinetics indicative of an off-pathway resting state. The resting-state structure of -CI from the thoracic muscle reveals multiple conformations. We identify a helix-locked state in which an N-terminal α-helix on the NDUFS4 subunit wedges between the peripheral and membrane arms. Comparison of the -CI structure and conformational states to those observed in bacteria, yeast, and mammals provides insight into the roles of subunits across organisms, explains why the -CI off-pathway resting state is NEM insensitive, and raises questions regarding current mechanistic models of complex I turnover. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 1.4 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3 MB | Display | ![]() |
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Full document | ![]() | 3.1 MB | Display | |
Data in XML | ![]() | 225.5 KB | Display | |
Data in CIF | ![]() | 337.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 28581MC ![]() 8eszC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
+NADH dehydrogenase ... , 29 types, 29 molecules ANS6S3V2S8A8A1AOS5AMBLB6B4B7B5B9BMB8B3C2B1S4A9V3V1A7A5A6AL
-Protein , 6 types, 7 molecules S1S7ACABB2S2A3
#3: Protein | Mass: 78724.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q94511, NADH:ubiquinone reductase (H+-translocating) | ||||||
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#6: Protein | Mass: 24622.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||
#26: Protein | Mass: 17257.992 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #31: Protein | | Mass: 10758.288 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #32: Protein | | Mass: 52985.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #40: Protein | | Mass: 8412.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-NADH-ubiquinone oxidoreductase chain ... , 7 types, 7 molecules 314524L6
#8: Protein | Mass: 13572.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P18930, NADH:ubiquinone reductase (H+-translocating) |
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#9: Protein | Mass: 36383.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: C7DZL9, NADH:ubiquinone reductase (H+-translocating) |
#10: Protein | Mass: 51383.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q9MDK5, NADH:ubiquinone reductase (H+-translocating) |
#11: Protein | Mass: 65777.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: C7DZL4, NADH:ubiquinone reductase (H+-translocating) |
#35: Protein | Mass: 39839.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P03896, NADH:ubiquinone reductase (H+-translocating) |
#36: Protein | Mass: 11363.853 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P18934, NADH:ubiquinone reductase (H+-translocating) |
#37: Protein | Mass: 20083.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P18933, NADH:ubiquinone reductase (H+-translocating) |
-Non-polymers , 10 types, 49 molecules ![](data/chem/img/CDL.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/PC1.gif)
![](data/chem/img/3PE.gif)
![](data/chem/img/ZMP.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/DGT.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/PC1.gif)
![](data/chem/img/3PE.gif)
![](data/chem/img/ZMP.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/DGT.gif)
#43: Chemical | ChemComp-CDL / #44: Chemical | ChemComp-ZN / | #45: Chemical | ChemComp-SF4 / #46: Chemical | #47: Chemical | ChemComp-PC1 / #48: Chemical | ChemComp-3PE / #49: Chemical | #50: Chemical | ChemComp-NDP / | #51: Chemical | ChemComp-FMN / | #52: Chemical | ChemComp-DGT / | |
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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 |
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Sample preparation
Component | Name: mitochondrial complex I from the thoracic muscles of D. melanogaster Type: COMPLEX / Entity ID: #1-#42 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 293389 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: OTHER | ||||||||||||||||||||||||
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