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- EMDB-17661: ACAD9 homodimer WT -

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Basic information

Entry
Database: EMDB / ID: EMD-17661
TitleACAD9 homodimer WT
Map dataACAD9 WT
Sample
  • Complex: ACAD9 WT
    • Protein or peptide: ACAD9 WT
KeywordsOxidative phosphorylation (OXPHOS) / Fatty Acid Oxidation (FAO) / Mitochondrial Complex I Assembly Complex (MCIA) / Amyloid-beta / SIGNALING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 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_17661.png

Downloads & links

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Map

FileDownload / File: emd_17661.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationACAD9 WT
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 211.712 Å		0.83 Å/pix.
x 256 pix.
= 211.712 Å		0.83 Å/pix.
x 256 pix.
= 211.712 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.827 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.100045025 - 0.20503196
Average (Standard dev.)0.0006246228 (±0.012120284)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 211.712 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: ACAD9 WT. Half A.

Fileemd_17661_half_map_1.map
AnnotationACAD9 WT. Half A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ACAD9 WT. Half B.

Fileemd_17661_half_map_2.map
AnnotationACAD9 WT. Half B.
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 WT

EntireName: ACAD9 WT
Components
  • Complex: ACAD9 WT
    • Protein or peptide: ACAD9 WT

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Supramolecule #1: ACAD9 WT

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

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Macromolecule #1: ACAD9 WT

MacromoleculeName: ACAD9 WT / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MAFAKELFLG KIKKKEVFPF PEVSQDELNE INQFLGPVEK FFTEEVDSRK IDQEGKIPDE TLEKLKSLGL FGLQVPEEYG GLGFSNTMYS RLGEIISMDG SITVTLAAHQ AIGLKGIILA GTEEQKAKYL PKLASGEHIA AFCLTEPASG SDAASIRSRA TLSEDKKHYI ...String:
MAFAKELFLG KIKKKEVFPF PEVSQDELNE INQFLGPVEK FFTEEVDSRK IDQEGKIPDE TLEKLKSLGL FGLQVPEEYG GLGFSNTMYS RLGEIISMDG SITVTLAAHQ AIGLKGIILA GTEEQKAKYL PKLASGEHIA AFCLTEPASG SDAASIRSRA TLSEDKKHYI LNGSKVWITN GGLANIFTVF AKTEVVDSDG SVKDKITAFI VERDFGGVTN GKPEDKLGIR GSNTCEVHFE NTKIPVENIL GEVGDGFKVA MNILNSGRFS MGSVVAGLLK RLIEMTAEYA CTRKQFNKRL SEFGLIQEKF ALMAQKAYVM ESMTYLTAGM LDQPGFPDCS IEAAMVKVFS SEAAWQCVSE ALQILGGLGY TRDYPYERIL RDTRILLIFE GTNEILRMYI ALTGLQHAGR ILTTRIHELK QAKVSTVMDT VGRRLRDSLG RTVDLGLTGN HGVVHPSLAD SANKFEENTY CFGRTVETLL LRFGKTIMEE QLVLKRVANI LINLYGMTAV LSRASRSIRI GLRNHDHEVL LANTFCVEAY LQNLFSLSQL DKYAPENLDE QIKKVSQQIL EKRAYICAHP LDRTCHHHHH H

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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 K2 SUMMIT (4k 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: 6.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 13287
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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