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- EMDB-25413: Structure of the NADH-bound human COQ7:COQ9 complex by single-par... -

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Basic information

Entry
Database: EMDB / ID: EMD-25413
TitleStructure of the NADH-bound human COQ7:COQ9 complex by single-particle electron cryo-microscopy
Map dataPostProcess Map
Sample
  • Complex: Human COQ7:COQ9 Complex
    • Protein or peptide: Ubiquinone biosynthesis protein COQ9, mitochondrial
    • Protein or peptide: 5-demethoxyubiquinone hydroxylase, mitochondrial
  • Ligand: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
  • Ligand: 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
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: water
Keywordshydroxylase / complex / lipid / enzyme / NADH / coenzymeQ / isoprene / OPP / MEMBRANE PROTEIN
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 / 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 / Ubiquinol biosynthesis / extrinsic component of mitochondrial inner membrane / 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
Ubiquinone biosynthesis protein Coq7 / Ubiquinone biosynthesis protein COQ9 / : / Ubiquinone biosynthesis protein COQ7 / Ubiquinone biosynthesis protein COQ9, N-terminal domain / COQ9 / COQ9 / Ferritin-like superfamily
Similarity search - Domain/homology
Ubiquinone biosynthesis protein COQ9, mitochondrial / 5-demethoxyubiquinone hydroxylase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsAydin H / Frost A
Funding support United States, 1 items
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, 2021-
Header (metadata) releaseNov 2, 2022-
Map releaseNov 2, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25413.png

Downloads & links

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Map

FileDownload / File: emd_25413.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostProcess Map
Voxel sizeX=Y=Z: 0.833 Å
Density
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.12826401 - 0.21909998
Average (Standard dev.)0.000027161403 (±0.009903074)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 213.248 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_25413_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Refine3D map

Fileemd_25413_additional_1.map
AnnotationRefine3D map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 1

Fileemd_25413_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_25413_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Human COQ7:COQ9 Complex

EntireName: Human COQ7:COQ9 Complex
Components
  • Complex: Human COQ7:COQ9 Complex
    • Protein or peptide: Ubiquinone biosynthesis protein COQ9, mitochondrial
    • Protein or peptide: 5-demethoxyubiquinone hydroxylase, mitochondrial
  • Ligand: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
  • Ligand: 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
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: water

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Supramolecule #1: Human COQ7:COQ9 Complex

SupramoleculeName: Human COQ7:COQ9 Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Ubiquinone biosynthesis protein COQ9, mitochondrial

MacromoleculeName: Ubiquinone biosynthesis protein COQ9, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.549945 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAAAAVSGAL GRAGWRLLQL RCLPVARCRQ ALVPRAFHAS AVGLRSSDEQ KQQPPNSFSQ QHSETQGAEK PDPESSHSPP RYTDQGGEE EEDYESEEQL QHRILTAALE FVPAHGWTAE AIAEGAQSLG LSSAAASMFG KDGSELILHF VTQCNTRLTR V LEEEQKLV ...String:
MAAAAVSGAL GRAGWRLLQL RCLPVARCRQ ALVPRAFHAS AVGLRSSDEQ KQQPPNSFSQ QHSETQGAEK PDPESSHSPP RYTDQGGEE EEDYESEEQL QHRILTAALE FVPAHGWTAE AIAEGAQSLG LSSAAASMFG KDGSELILHF VTQCNTRLTR V LEEEQKLV QLGQAEKRKT DQFLRDAVET RLRMLIPYIE HWPRALSILM LPHNIPSSLS LLTSMVDDMW HYAGDQSTDF NW YTRRAML AAIYNTTELV MMQDSSPDFE DTWRFLENRV NDAMNMGHTA KQVKSTGEAL VQGLMGAAVT LKNLTGLNQR R

UniProtKB: Ubiquinone biosynthesis protein COQ9, mitochondrial

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Macromolecule #2: 5-demethoxyubiquinone hydroxylase, mitochondrial

MacromoleculeName: 5-demethoxyubiquinone hydroxylase, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: 3-demethoxyubiquinol 3-hydroxylase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.313064 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSCAGAAAAP RLWRLRPGAR RSLSAYGRRT SVRFRSSGMT LDNISRAAVD RIIRVDHAGE YGANRIYAGQ MAVLGRTSVG PVIQKMWDQ EKDHLKKFNE LMVTFRVRPT VLMPLWNVLG FALGAGTALL GKEGAMACTV AVEESIAHHY NNQIRTLMEE D PEKYEELL ...String:
MSCAGAAAAP RLWRLRPGAR RSLSAYGRRT SVRFRSSGMT LDNISRAAVD RIIRVDHAGE YGANRIYAGQ MAVLGRTSVG PVIQKMWDQ EKDHLKKFNE LMVTFRVRPT VLMPLWNVLG FALGAGTALL GKEGAMACTV AVEESIAHHY NNQIRTLMEE D PEKYEELL QLIKKFRDEE LEHHDIGLDH DAELAPAYAV LKSIIQAGCR VAIYLSERL

UniProtKB: 5-demethoxyubiquinone hydroxylase, mitochondrial

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Macromolecule #3: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY...

MacromoleculeName: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
type: ligand / ID: 3 / Number of copies: 32 / Formula: PEV
Molecular weightTheoretical: 720.012 Da
Chemical component information

ChemComp-PEV:
(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / POPE, phospholipid*YM

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Macromolecule #4: 2-[(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDO...

MacromoleculeName: 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
type: ligand / ID: 4 / Number of copies: 4 / Formula: 8PP
Molecular weightTheoretical: 639.047 Da
Chemical component information

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

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Macromolecule #5: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

MacromoleculeName: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 5 / Number of copies: 2 / Formula: NAD
Molecular weightTheoretical: 663.425 Da
Chemical component information

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 170 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 372917
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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