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Yorodumi- PDB-7ssp: Structure of the human COQ7:COQ9 complex by single-particle elect... -
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-Basic information
Entry | Database: PDB / ID: 7ssp | ||||||
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Title | Structure of the human COQ7:COQ9 complex by single-particle electron cryo-microscopy, unliganded state | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / hydroxylase / complex / lipid / enzyme | ||||||
Function / homology | Function and homology information 3-demethoxyubiquinol 3-hydroxylase / 3-demethoxyubiquinol 3-hydroxylase activity / extrinsic component of mitochondrial inner membrane / Ubiquinol biosynthesis / ubiquinone biosynthesis complex / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / ubiquinone biosynthetic process / regulation of reactive oxygen species metabolic process / mitochondrial electron transport, NADH to ubiquinone / determination of adult lifespan ...3-demethoxyubiquinol 3-hydroxylase / 3-demethoxyubiquinol 3-hydroxylase activity / extrinsic component of mitochondrial inner membrane / Ubiquinol biosynthesis / ubiquinone biosynthesis complex / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / ubiquinone biosynthetic process / regulation of reactive oxygen species metabolic process / mitochondrial electron transport, NADH to ubiquinone / determination of adult lifespan / chromosome / regulation of gene expression / mitochondrial inner membrane / lipid binding / chromatin binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Aydin, H. / Frost, A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Mol Cell / Year: 2022 Title: Structure and functionality of a multimeric human COQ7:COQ9 complex. Authors: Mateusz Manicki / Halil Aydin / Luciano A Abriata / Katherine A Overmyer / Rachel M Guerra / Joshua J Coon / Matteo Dal Peraro / Adam Frost / David J Pagliarini / Abstract: Coenzyme Q (CoQ) is a redox-active lipid essential for core metabolic pathways and antioxidant defense. CoQ is synthesized upon the mitochondrial inner membrane by an ill-defined "complex Q" ...Coenzyme Q (CoQ) is a redox-active lipid essential for core metabolic pathways and antioxidant defense. CoQ is synthesized upon the mitochondrial inner membrane by an ill-defined "complex Q" metabolon. Here, we present structure-function analyses of a lipid-, substrate-, and NADH-bound complex comprising two complex Q subunits: the hydroxylase COQ7 and the lipid-binding protein COQ9. We reveal that COQ7 adopts a ferritin-like fold with a hydrophobic channel whose substrate-binding capacity is enhanced by COQ9. Using molecular dynamics, we further show that two COQ7:COQ9 heterodimers form a curved tetramer that deforms the membrane, potentially opening a pathway for the CoQ intermediates to translocate from the bilayer to the proteins' lipid-binding sites. Two such tetramers assemble into a soluble octamer with a pseudo-bilayer of lipids captured within. Together, these observations indicate that COQ7 and COQ9 cooperate to access hydrophobic precursors within the membrane and coordinate subsequent synthesis steps toward producing CoQ. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
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PDBx/mmCIF format | 7ssp.cif.gz | 294.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ssp.ent.gz | 229.4 KB | Display | PDB format |
PDBx/mmJSON format | 7ssp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ssp_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7ssp_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7ssp_validation.xml.gz | 45.1 KB | Display | |
Data in CIF | 7ssp_validation.cif.gz | 68.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ss/7ssp ftp://data.pdbj.org/pub/pdb/validation_reports/ss/7ssp | HTTPS FTP |
-Related structure data
Related structure data | 25412MC 7sssC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 35549.945 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: COQ9, C16orf49, HSPC326, PSEC0129 / Production host: Escherichia coli (E. coli) / References: UniProt: O75208 #2: Protein | Mass: 24313.064 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: COQ7 / Production host: Escherichia coli (E. coli) References: UniProt: Q99807, 3-demethoxyubiquinol 3-hydroxylase |
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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
Component | Name: Human COQ7:COQ9 Complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 58.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.15.2_3472: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: D2 (2x2 fold dihedral) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61526 / Symmetry type: POINT | ||||||||||||||||||||||||
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