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- PDB-7sss: Structure of the NADH-bound human COQ7:COQ9 complex by single-par... -

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Basic information

Entry
Database: PDB / ID: 7sss
TitleStructure of the NADH-bound human COQ7:COQ9 complex by single-particle electron cryo-microscopy
Components
  • 5-demethoxyubiquinone hydroxylase, mitochondrial
  • Ubiquinone biosynthesis protein COQ9, mitochondrialCoenzyme Q10
KeywordsMEMBRANE PROTEIN / hydroxylase / complex / lipid / enzyme / NADH / coenzymeQ / isoprene / OPP
Function / homology
Function and homology information


3-demethoxyubiquinol 3-hydroxylase / 3-demethoxyubiquinol 3-hydroxylase activity / Ubiquinol biosynthesis / extrinsic component of mitochondrial inner membrane / ubiquinone biosynthesis complex / ubiquinone biosynthetic process / 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 / mitochondrial electron transport, NADH to ubiquinone / determination of adult lifespan ...3-demethoxyubiquinol 3-hydroxylase / 3-demethoxyubiquinol 3-hydroxylase activity / Ubiquinol biosynthesis / extrinsic component of mitochondrial inner membrane / ubiquinone biosynthesis complex / ubiquinone biosynthetic process / 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 / 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 COQ9 / : / Ubiquinone biosynthesis protein COQ9, N-terminal domain / COQ9 / COQ9 / Ferritin-like superfamily
Similarity search - Domain/homology
Chem-8PP / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-PEV / Ubiquinone biosynthesis protein COQ9, mitochondrial / 5-demethoxyubiquinone hydroxylase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 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
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 30, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)266,37546
Polymers239,4528
Non-polymers26,92338
Water3,063170
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area38420 Å2
ΔGint-305 kcal/mol
Surface area59190 Å2

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Components

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Protein , 2 types, 8 molecules ABCDEFGH

#1: Protein
Ubiquinone biosynthesis protein COQ9, mitochondrial / Coenzyme Q10


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, 3-demethoxyubiquinol 3-hydroxylase

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Non-polymers , 4 types, 208 molecules

#3: Chemical...
ChemComp-PEV / (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLETHANOLAMINE / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Phosphatidylethanolamine


Mass: 720.012 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C39H78NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: POPE, phospholipid*YM
#4: Chemical
ChemComp-8PP / 2-[(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL]PHENOL


Mass: 639.047 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C46H70O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: #1-#2 / 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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1200 nm / Nominal defocus min: 300 nm
Image recordingElectron dose: 65 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.1_4122: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 372917 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00812225
ELECTRON MICROSCOPYf_angle_d1.09216442
ELECTRON MICROSCOPYf_dihedral_angle_d14.5964561
ELECTRON MICROSCOPYf_chiral_restr0.0431778
ELECTRON MICROSCOPYf_plane_restr0.0192066

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