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- EMDB-12055: ACAD9-ECSIT-CTD (ACAD9 core) -

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Basic information

Entry
Database: EMDB / ID: EMD-12055
TitleACAD9-ECSIT-CTD (ACAD9 core)
Map dataACAD9-ECSIT-Cter (ACAD9 core) sharpened map
Sample
  • Complex: Complex between ACAD9 and a C-terminal construct of ECSIT
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.8 Å
AuthorsGiachin G / Jessop M / Soler-Lopez M / Gutsche I
Funding support1 items
OrganizationGrant numberCountry
European Research Council (ERC)647784
CitationJournal: Angew Chem Int Ed Engl / Year: 2021
Title: Assembly of The Mitochondrial Complex I Assembly Complex Suggests a Regulatory Role for Deflavination.
Authors: Gabriele Giachin / Matthew Jessop / Romain Bouverot / Samira Acajjaoui / Melissa Saïdi / Anaïs Chretien / Maria Bacia-Verloop / Luca Signor / Philippe J Mas / Adrien Favier / Eve Borel ...Authors: Gabriele Giachin / Matthew Jessop / Romain Bouverot / Samira Acajjaoui / Melissa Saïdi / Anaïs Chretien / Maria Bacia-Verloop / Luca Signor / Philippe J Mas / Adrien Favier / Eve Borel Meneroud / Michael Hons / Darren J Hart / Eaazhisai Kandiah / Elisabetta Boeri Erba / Alain Buisson / Gordon Leonard / Irina Gutsche / Montserrat Soler-Lopez /
Abstract: Fatty acid β-oxidation (FAO) and oxidative phosphorylation (OXPHOS) are mitochondrial redox processes that generate ATP. The biogenesis of the respiratory Complex I, a 1 MDa multiprotein complex ...Fatty acid β-oxidation (FAO) and oxidative phosphorylation (OXPHOS) are mitochondrial redox processes that generate ATP. The biogenesis of the respiratory Complex I, a 1 MDa multiprotein complex that is responsible for initiating OXPHOS, is mediated by assembly factors including the mitochondrial complex I assembly (MCIA) complex. However, the organisation and the role of the MCIA complex are still unclear. Here we show that ECSIT functions as the bridging node of the MCIA core complex. Furthermore, cryo-electron microscopy together with biochemical and biophysical experiments reveal that the C-terminal domain of ECSIT directly binds to the vestigial dehydrogenase domain of the FAO enzyme ACAD9 and induces its deflavination, switching ACAD9 from its role in FAO to an MCIA factor. These findings provide the structural basis for the MCIA complex architecture and suggest a unique molecular mechanism for coordinating the regulation of the FAO and OXPHOS pathways to ensure an efficient energy production.
History
DepositionDec 8, 2020-
Header (metadata) releaseDec 30, 2020-
Map releaseDec 30, 2020-
UpdateMar 3, 2021-
Current statusMar 3, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.38
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.38
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12055.png

Downloads & links

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Map

FileDownload / File: emd_12055.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationACAD9-ECSIT-Cter (ACAD9 core) sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 160 pix.
= 170.72 Å		1.07 Å/pix.
x 160 pix.
= 170.72 Å		1.07 Å/pix.
x 160 pix.
= 170.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.067 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.38 / Movie #1: 0.38
Minimum - Maximum-1.4538845 - 2.2421217
Average (Standard dev.)0.01710861 (±0.08622573)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 170.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0671.0671.067
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z170.720170.720170.720
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-1.4542.2420.017

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Supplemental data

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Mask #1

Fileemd_12055_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ACAD9-ECSIT-Cter (ACAD9 core) half map A

Fileemd_12055_half_map_1.map
AnnotationACAD9-ECSIT-Cter (ACAD9 core) half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ACAD9-ECSIT-Cter (ACAD9 core) half map B

Fileemd_12055_half_map_2.map
AnnotationACAD9-ECSIT-Cter (ACAD9 core) half map 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 : Complex between ACAD9 and a C-terminal construct of ECSIT

EntireName: Complex between ACAD9 and a C-terminal construct of ECSIT
Components
  • Complex: Complex between ACAD9 and a C-terminal construct of ECSIT

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Supramolecule #1: Complex between ACAD9 and a C-terminal construct of ECSIT

SupramoleculeName: Complex between ACAD9 and a C-terminal construct of ECSIT
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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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
GridModel: Quantifoil R2/1 / Material: COPPER/RHODIUM / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
Details: Grids were pumped for 1 hour under vacuum prior to freezing..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 41.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 700000
CTF correctionSoftware - Name: Gctf
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 7.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 16000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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