[English] 日本語
![](img/lk-miru.gif)
- PDB-7sss: Structure of the NADH-bound human COQ7:COQ9 complex by single-par... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7sss | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the NADH-bound human COQ7:COQ9 complex by single-particle electron cryo-microscopy | ||||||
![]() |
| ||||||
![]() | MEMBRANE PROTEIN / hydroxylase / complex / lipid / enzyme / NADH / coenzymeQ / isoprene / OPP | ||||||
Function / homology | ![]() 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 / regulation of reactive oxygen species metabolic process / ubiquinone biosynthetic 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 / regulation of reactive oxygen species metabolic process / ubiquinone biosynthetic process / mitochondrial electron transport, NADH to ubiquinone / determination of adult lifespan / chromosome / regulation of gene expression / mitochondrial inner membrane / chromatin binding / lipid binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / mitochondrion / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å | ||||||
![]() | Aydin, H. / Frost, A. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 331.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 254.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.4 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2.4 MB | Display | |
Data in XML | ![]() | 62.3 KB | Display | |
Data in CIF | ![]() | 83.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 25413MC ![]() 7sspC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
-Protein , 2 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 35549.945 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 24313.064 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q99807, 3-demethoxyubiquinol 3-hydroxylase |
---|
-Non-polymers , 4 types, 208 molecules ![](data/chem/img/PEV.gif)
![](data/chem/img/8PP.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/8PP.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-PEV / ( #4: Chemical | ChemComp-8PP / #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: Human COQ7:COQ9 Complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
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: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1200 nm / Nominal defocus min: 300 nm |
Image recording | Electron dose: 65 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-
Processing
Software | Name: PHENIX / Version: 1.19.1_4122: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 372917 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|