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- PDB-7ssp: Structure of the human COQ7:COQ9 complex by single-particle elect... -

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Basic information

Entry
Database: PDB / ID: 7ssp
TitleStructure of the human COQ7:COQ9 complex by single-particle electron cryo-microscopy, unliganded state
Components
  • 5-demethoxyubiquinone hydroxylase, mitochondrial
  • Ubiquinone biosynthesis protein COQ9, mitochondrial
KeywordsMEMBRANE PROTEIN / hydroxylase / complex / lipid / enzyme
Function / homology
Function and homology information


3-demethoxyubiquinone 3-hydroxylase (NADH) / 3-demethoxyubiquinol 3-hydroxylase activity / 3-demethoxyubiquinone 3-hydroxylase (NADH) activity / extrinsic component of mitochondrial inner membrane / Ubiquinol biosynthesis / ubiquinone biosynthesis complex / isoprenoid binding / ubiquinone biosynthetic process / regulation of reactive oxygen species metabolic process / mitochondrial electron transport, NADH to ubiquinone ...3-demethoxyubiquinone 3-hydroxylase (NADH) / 3-demethoxyubiquinol 3-hydroxylase activity / 3-demethoxyubiquinone 3-hydroxylase (NADH) activity / extrinsic component of mitochondrial inner membrane / Ubiquinol biosynthesis / ubiquinone biosynthesis complex / isoprenoid binding / 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 / metal ion binding / nucleus
Similarity search - Function
Ubiquinone biosynthesis protein Coq7 / Ubiquinone biosynthesis protein COQ7 / Ubiquinone biosynthesis protein COQ9 / : / Ubiquinone biosynthesis protein COQ9, N-terminal domain / COQ9 / COQ9 / Ferritin-like superfamily
Similarity search - Domain/homology
Ubiquinone biosynthesis protein COQ9, mitochondrial / NADPH-dependent 3-demethoxyubiquinone 3-hydroxylase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsAydin, H. / Frost, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM127673-04 United States
CitationJournal: 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
DepositionNov 11, 2021Deposition site: RCSB / Processing site: RCSB
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquinone biosynthesis protein COQ9, mitochondrial
B: Ubiquinone biosynthesis protein COQ9, mitochondrial
C: Ubiquinone biosynthesis protein COQ9, mitochondrial
D: Ubiquinone biosynthesis protein COQ9, mitochondrial
E: 5-demethoxyubiquinone hydroxylase, mitochondrial
F: 5-demethoxyubiquinone hydroxylase, mitochondrial
G: 5-demethoxyubiquinone hydroxylase, mitochondrial
H: 5-demethoxyubiquinone hydroxylase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)239,4528
Polymers239,4528
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area9620 Å2
ΔGint-71 kcal/mol
Surface area71870 Å2

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Components

#1: Protein
Ubiquinone biosynthesis protein COQ9, mitochondrial


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
5-demethoxyubiquinone hydroxylase, mitochondrial / DMQ hydroxylase / Timing protein clk-1 homolog / Ubiquinone biosynthesis monooxygenase COQ7


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, EC: 1.14.99.60
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human COQ7:COQ9 Complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 58.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61526 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00311138
ELECTRON MICROSCOPYf_angle_d0.55515078
ELECTRON MICROSCOPYf_dihedral_angle_d8.2736716
ELECTRON MICROSCOPYf_chiral_restr0.0371696
ELECTRON MICROSCOPYf_plane_restr0.0051940

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