[English] 日本語
Yorodumi
- EMDB-17659: ACAD9-WT in complex with ECSIT-CTER -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-17659
TitleACAD9-WT in complex with ECSIT-CTER
Map dataACAD9 homodimer in complex with two ECSIT C-terminal monomers.
Sample
  • Complex: ACAD9 WT in complex with ECSIT CTER
    • Protein or peptide: Complex I assembly factor ACAD9, mitochondrial
    • Protein or peptide: Evolutionarily conserved signaling intermediate in Toll pathway, mitochondrial
  • Ligand: water
KeywordsOxidative phosphorylation (OXPHOS) / Fatty Acid Oxidation (FAO) / Mitochondrial Complex I Assembly Complex (MCIA) / Amyloid-beta / ECSIT phosphorylation / SIGNALING PROTEIN
Function / homology
Function and homology information


regulation of oxidoreductase activity / 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 / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / MyD88 cascade initiated on plasma membrane ...regulation of oxidoreductase activity / 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 / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / MyD88 cascade initiated on plasma membrane / regulation of protein complex stability / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / cell surface receptor protein serine/threonine kinase signaling pathway / mitochondrial respiratory chain complex I assembly / mitochondrial membrane / flavin adenine dinucleotide binding / mitochondrial inner membrane / molecular adaptor activity / innate immune response / dendrite / mitochondrion / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
ECSIT / ECSIT, C-terminal domain / ECSIT, N-terminal / Evolutionarily conserved signalling intermediate in Toll pathway / C-terminal domain of the ECSIT protein / C-terminal domain of the ECSIT protein / : / ACAD9/ACADV, C-terminal domain / Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. ...ECSIT / ECSIT, C-terminal domain / ECSIT, N-terminal / Evolutionarily conserved signalling intermediate in Toll pathway / C-terminal domain of the ECSIT protein / C-terminal domain of the ECSIT protein / : / ACAD9/ACADV, C-terminal domain / Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal
Similarity search - Domain/homology
Evolutionarily conserved signaling intermediate in Toll pathway, mitochondrial / Complex I assembly factor ACAD9, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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

-
Structure visualization

Supplemental images

emd_17659.png

Downloads & links

-
Map

FileDownload / File: emd_17659.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationACAD9 homodimer in complex with two ECSIT C-terminal monomers.
Voxel sizeX=Y=Z: 0.827 Å
Density
Contour LevelBy AUTHOR: 0.69
Minimum - Maximum-2.6842556 - 4.294613
Average (Standard dev.)0.0038805057 (±0.118912764)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Half map: ACAD9 homodimer in complex with two ECSIT C-terminal...

Fileemd_17659_half_map_1.map
AnnotationACAD9 homodimer in complex with two ECSIT C-terminal monomers. Half Map B.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: ACAD9 homodimer in complex with two ECSIT C-terminal...

Fileemd_17659_half_map_2.map
AnnotationACAD9 homodimer in complex with two ECSIT C-terminal monomers. Half Map A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : ACAD9 WT in complex with ECSIT CTER

EntireName: ACAD9 WT in complex with ECSIT CTER
Components
  • Complex: ACAD9 WT in complex with ECSIT CTER
    • Protein or peptide: Complex I assembly factor ACAD9, mitochondrial
    • Protein or peptide: Evolutionarily conserved signaling intermediate in Toll pathway, mitochondrial
  • Ligand: water

-
Supramolecule #1: ACAD9 WT in complex with ECSIT CTER

SupramoleculeName: ACAD9 WT in complex with ECSIT CTER / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 180 KDa

-
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: 65.858523 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAFAKELFLG KIKKKEVFPF PEVSQDELNE INQFLGPVEK FFTEEVDSRK IDQEGKIPDE TLEKLKSLGL FGLQVPEEYG GLGFSNTMY SRLGEIISMD GSITVTLAAH QAIGLKGIIL AGTEEQKAKY LPKLASGEHI AAFCLTEPAS GSDAASIRSR A TLSEDKKH ...String:
MAFAKELFLG KIKKKEVFPF PEVSQDELNE INQFLGPVEK FFTEEVDSRK IDQEGKIPDE TLEKLKSLGL FGLQVPEEYG GLGFSNTMY SRLGEIISMD GSITVTLAAH QAIGLKGIIL AGTEEQKAKY LPKLASGEHI AAFCLTEPAS GSDAASIRSR 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

-
Macromolecule #2: Evolutionarily conserved signaling intermediate in Toll pathway, ...

MacromoleculeName: Evolutionarily conserved signaling intermediate in Toll pathway, mitochondrial
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.240031 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGQDPVELAM FGLRHMEPDL SARVTIYQVP LPKDSTGAAD PPQPHIVGIQ SPDQQAALAR HNPARPVFVE GPFSLWLRNK CVYYHILRA DLLPPEEREV EETPEEWNLY YPMQLDLEYV RSGWDNYEFD INEVEEGPVF AMCMAGAHDQ ATMAKWIQGL Q ETNPTLAQ ...String:
MGQDPVELAM FGLRHMEPDL SARVTIYQVP LPKDSTGAAD PPQPHIVGIQ SPDQQAALAR HNPARPVFVE GPFSLWLRNK CVYYHILRA DLLPPEEREV EETPEEWNLY YPMQLDLEYV RSGWDNYEFD INEVEEGPVF AMCMAGAHDQ ATMAKWIQGL Q ETNPTLAQ IPVVFRLAGS TRELQTSSAG LEEPPLPEDH QEEDDNLQRQ QQGQSLEHHH HHH

UniProtKB: Evolutionarily conserved signaling intermediate in Toll pathway, mitochondrial

-
Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 38 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 279483

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more