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- EMDB-17660: Cryo-EM structure of human ACAD9-S191A -

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Basic information

Entry
Database: EMDB / ID: EMD-17660
TitleCryo-EM structure of human ACAD9-S191A
Map dataACAD9 mutant S191A
Sample
  • Complex: ACAD9 S191A
    • Protein or peptide: Complex I assembly factor ACAD9, mitochondrial
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
KeywordsOxidative phosphorylation (OXPHOS) / Fatty Acid Oxidation (FAO) / Mitochondrial Complex I Assembly Complex (MCIA) / Amyloid-beta / SIGNALING PROTEIN / FLAVOPROTEIN
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors; With a flavin as acceptor / long-chain fatty acyl-CoA dehydrogenase activity / medium-chain fatty acyl-CoA dehydrogenase activity / medium-chain fatty acid metabolic process / long-chain fatty acid metabolic process / Complex I biogenesis / acyl-CoA dehydrogenase activity / mitochondrial respiratory chain complex I assembly / mitochondrial membrane / flavin adenine dinucleotide binding ...Oxidoreductases; Acting on the CH-CH group of donors; With a flavin as acceptor / long-chain fatty acyl-CoA dehydrogenase activity / medium-chain fatty acyl-CoA dehydrogenase activity / medium-chain fatty acid metabolic process / long-chain fatty acid metabolic process / Complex I biogenesis / acyl-CoA dehydrogenase activity / mitochondrial respiratory chain complex I assembly / mitochondrial membrane / flavin adenine dinucleotide binding / mitochondrial inner membrane / dendrite / mitochondrion / nucleus
Similarity search - Function
: / ACAD9/ACADV, C-terminal domain / Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain ...: / ACAD9/ACADV, C-terminal domain / Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal
Similarity search - Domain/homology
Complex I assembly factor ACAD9, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsMcGregor L / Acajjaoui S / Desfosses A / Saidi M / Bacia-Verloop M / Schwarz JJ / Juyoux P / Von Velsen J / Bowler MW / McCarthy A ...McGregor L / Acajjaoui S / Desfosses A / Saidi M / Bacia-Verloop M / Schwarz JJ / Juyoux P / Von Velsen J / Bowler MW / McCarthy A / Kandiah E / Gutsche I / Soler-Lopez M
Funding support France, 1 items
OrganizationGrant numberCountry
Other government France
CitationJournal: Nat Commun / Year: 2023
Title: The assembly of the Mitochondrial Complex I Assembly complex uncovers a redox pathway coordination.
Authors: Lindsay McGregor / Samira Acajjaoui / Ambroise Desfosses / Melissa Saïdi / Maria Bacia-Verloop / Jennifer J Schwarz / Pauline Juyoux / Jill von Velsen / Matthew W Bowler / Andrew A McCarthy ...Authors: Lindsay McGregor / Samira Acajjaoui / Ambroise Desfosses / Melissa Saïdi / Maria Bacia-Verloop / Jennifer J Schwarz / Pauline Juyoux / Jill von Velsen / Matthew W Bowler / Andrew A McCarthy / Eaazhisai Kandiah / Irina Gutsche / Montserrat Soler-Lopez /
Abstract: The Mitochondrial Complex I Assembly (MCIA) complex is essential for the biogenesis of respiratory Complex I (CI), the first enzyme in the respiratory chain, which has been linked to Alzheimer's ...The Mitochondrial Complex I Assembly (MCIA) complex is essential for the biogenesis of respiratory Complex I (CI), the first enzyme in the respiratory chain, which has been linked to Alzheimer's disease (AD) pathogenesis. However, how MCIA facilitates CI assembly, and how it is linked with AD pathogenesis, is poorly understood. Here we report the structural basis of the complex formation between the MCIA subunits ECSIT and ACAD9. ECSIT binding induces a major conformational change in the FAD-binding loop of ACAD9, releasing the FAD cofactor and converting ACAD9 from a fatty acid β-oxidation (FAO) enzyme to a CI assembly factor. We provide evidence that ECSIT phosphorylation downregulates its association with ACAD9 and is reduced in neuronal cells upon exposure to amyloid-β (Aβ) oligomers. These findings advance our understanding of the MCIA complex assembly and suggest a possible role for ECSIT in the reprogramming of bioenergetic pathways linked to Aβ toxicity, a hallmark of AD.
History
DepositionJun 19, 2023-
Header (metadata) releaseJan 24, 2024-
Map releaseJan 24, 2024-
UpdateJan 31, 2024-
Current statusJan 31, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17660.png

Downloads & links

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Map

FileDownload / File: emd_17660.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationACAD9 mutant S191A
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 256 pix.
= 215.04 Å		0.84 Å/pix.
x 256 pix.
= 215.04 Å		0.84 Å/pix.
x 256 pix.
= 215.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.66
Minimum - Maximum-2.6930952 - 4.2119665
Average (Standard dev.)0.00391449 (±0.10284014)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 215.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: ACAD9 mutant S191A. Half B.

Fileemd_17660_half_map_1.map
AnnotationACAD9 mutant S191A. Half B.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ACAD9 mutant S191A. Half A.

Fileemd_17660_half_map_2.map
AnnotationACAD9 mutant S191A. Half A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ACAD9 S191A

EntireName: ACAD9 S191A
Components
  • Complex: ACAD9 S191A
    • Protein or peptide: Complex I assembly factor ACAD9, mitochondrial
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE

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Supramolecule #1: ACAD9 S191A

SupramoleculeName: ACAD9 S191A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 120 KDa

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Macromolecule #1: Complex I assembly factor ACAD9, mitochondrial

MacromoleculeName: Complex I assembly factor ACAD9, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: Oxidoreductases; Acting on the CH-CH group of donors; With a flavin as acceptor
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 65.842523 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAFAKELFLG KIKKKEVFPF PEVSQDELNE INQFLGPVEK FFTEEVDSRK IDQEGKIPDE TLEKLKSLGL FGLQVPEEYG GLGFSNTMY SRLGEIISMD GSITVTLAAH QAIGLKGIIL AGTEEQKAKY LPKLASGEHI AAFCLTEPAS GSDAAAIRSR A TLSEDKKH ...String:
MAFAKELFLG KIKKKEVFPF PEVSQDELNE INQFLGPVEK FFTEEVDSRK IDQEGKIPDE TLEKLKSLGL FGLQVPEEYG GLGFSNTMY SRLGEIISMD GSITVTLAAH QAIGLKGIIL AGTEEQKAKY LPKLASGEHI AAFCLTEPAS GSDAAAIRSR A TLSEDKKH YILNGSKVWI TNGGLANIFT VFAKTEVVDS DGSVKDKITA FIVERDFGGV TNGKPEDKLG IRGSNTCEVH FE NTKIPVE NILGEVGDGF KVAMNILNSG RFSMGSVVAG LLKRLIEMTA EYACTRKQFN KRLSEFGLIQ EKFALMAQKA YVM ESMTYL TAGMLDQPGF PDCSIEAAMV KVFSSEAAWQ CVSEALQILG GLGYTRDYPY ERILRDTRIL LIFEGTNEIL RMYI ALTGL QHAGRILTTR IHELKQAKVS TVMDTVGRRL RDSLGRTVDL GLTGNHGVVH PSLADSANKF EENTYCFGRT VETLL LRFG KTIMEEQLVL KRVANILINL YGMTAVLSRA SRSIRIGLRN HDHEVLLANT FCVEAYLQNL FSLSQLDKYA PENLDE QIK KVSQQILEKR AYICAHPLDR TCHHHHHH

UniProtKB: Complex I assembly factor ACAD9, mitochondrial

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Macromolecule #2: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 2 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 163409
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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