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- EMDB-40463: human liver mitochondrial Medium-chain specific acyl-CoA dehydrogenase -

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Basic information

Entry
Database: EMDB / ID: EMD-40463
Titlehuman liver mitochondrial Medium-chain specific acyl-CoA dehydrogenase
Map data
Sample
  • Complex: Medium-chain specific acyl-CoA dehydrogenase
    • Protein or peptide: Medium-chain specific acyl-CoA dehydrogenase, mitochondrial
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
Keywordshuman / liver / mitochondrial / Medium-chain specific acyl-CoA dehydrogenase / OXIDOREDUCTASE
Function / homology
Function and homology information


medium-chain fatty acid catabolic process / mitochondrial fatty acid beta-oxidation of unsaturated fatty acids / carnitine metabolic process, CoA-linked / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / medium-chain acyl-CoA dehydrogenase / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / medium-chain fatty acyl-CoA dehydrogenase activity / carnitine biosynthetic process / medium-chain fatty acid metabolic process / fatty acid beta-oxidation using acyl-CoA dehydrogenase ...medium-chain fatty acid catabolic process / mitochondrial fatty acid beta-oxidation of unsaturated fatty acids / carnitine metabolic process, CoA-linked / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / medium-chain acyl-CoA dehydrogenase / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / medium-chain fatty acyl-CoA dehydrogenase activity / carnitine biosynthetic process / medium-chain fatty acid metabolic process / fatty acid beta-oxidation using acyl-CoA dehydrogenase / acyl-CoA dehydrogenase activity / cardiac muscle cell differentiation / glycogen biosynthetic process / regulation of gluconeogenesis / fatty acid beta-oxidation / response to starvation / response to cold / post-embryonic development / liver development / mitochondrial membrane / PPARA activates gene expression / flavin adenine dinucleotide binding / mitochondrial matrix / axon / mitochondrion / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Medium-chain specific acyl-CoA dehydrogenase / : / 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 ...Medium-chain specific acyl-CoA dehydrogenase / : / 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
Medium-chain specific acyl-CoA dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.69 Å
AuthorsZhang Z
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI145069 United States
CitationJournal: Mol Cell Proteomics / Year: 2023
Title: High-Resolution Structural Proteomics of Mitochondria Using the 'Build and Retrieve' Methodology.
Authors: Zhemin Zhang / Marios L Tringides / Christopher E Morgan / Masaru Miyagi / Jason A Mears / Charles L Hoppel / Edward W Yu /
Abstract: The application of integrated systems biology to the field of structural biology is a promising new direction, although it is still in the infant stages of development. Here we report the use of ...The application of integrated systems biology to the field of structural biology is a promising new direction, although it is still in the infant stages of development. Here we report the use of single particle cryo-EM to identify multiple proteins from three enriched heterogeneous fractions prepared from human liver mitochondrial lysate. We simultaneously identify and solve high-resolution structures of nine essential mitochondrial enzymes with key metabolic functions, including fatty acid catabolism, reactive oxidative species clearance, and amino acid metabolism. Our methodology also identified multiple distinct members of the acyl-CoA dehydrogenase family. This work highlights the potential of cryo-EM to explore tissue proteomics at the atomic level.
History
DepositionApr 12, 2023-
Header (metadata) releaseFeb 21, 2024-
Map releaseFeb 21, 2024-
UpdateFeb 21, 2024-
Current statusFeb 21, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40463.png

Downloads & links

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Map

FileDownload / File: emd_40463.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 352 pix.
= 290.576 Å		0.83 Å/pix.
x 352 pix.
= 290.576 Å		0.83 Å/pix.
x 352 pix.
= 290.576 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8255 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.30833545 - 0.80342007
Average (Standard dev.)0.0021540914 (±0.020115266)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 290.576 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_40463_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #2

Fileemd_40463_half_map_2.map
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Sample components

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Entire : Medium-chain specific acyl-CoA dehydrogenase

EntireName: Medium-chain specific acyl-CoA dehydrogenase
Components
  • Complex: Medium-chain specific acyl-CoA dehydrogenase
    • Protein or peptide: Medium-chain specific acyl-CoA dehydrogenase, mitochondrial
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE

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Supramolecule #1: Medium-chain specific acyl-CoA dehydrogenase

SupramoleculeName: Medium-chain specific acyl-CoA dehydrogenase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Medium-chain specific acyl-CoA dehydrogenase, mitochondrial

MacromoleculeName: Medium-chain specific acyl-CoA dehydrogenase, mitochondrial
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: medium-chain acyl-CoA dehydrogenase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.648273 KDa
SequenceString: MAAGFGRCCR VLRSISRFHW RSQHTKANRQ REPGLGFSFE FTEQQKEFQA TARKFAREEI IPVAAEYDKT GEYPVPLIRR AWELGLMNT HIPENCGGLG LGTFDACLIS EELAYGCTGV QTAIEGNSLG QMPIIIAGND QQKKKYLGRM TEEPLMCAYC V TEPGAGSD ...String:
MAAGFGRCCR VLRSISRFHW RSQHTKANRQ REPGLGFSFE FTEQQKEFQA TARKFAREEI IPVAAEYDKT GEYPVPLIRR AWELGLMNT HIPENCGGLG LGTFDACLIS EELAYGCTGV QTAIEGNSLG QMPIIIAGND QQKKKYLGRM TEEPLMCAYC V TEPGAGSD VAGIKTKAEK KGDEYIINGQ KMWITNGGKA NWYFLLARSD PDPKAPANKA FTGFIVEADT PGIQIGRKEL NM GQRCSDT RGIVFEDVKV PKENVLIGDG AGFKVAMGAF DKTRPVVAAG AVGLAQRALD EATKYALERK TFGKLLVEHQ AIS FMLAEM AMKVELARMS YQRAAWEVDS GRRNTYYASI AKAFAGDIAN QLATDAVQIL GGNGFNTEYP VEKLMRDAKI YQIY EGTSQ IQRLIVAREH IDKYKN

UniProtKB: Medium-chain specific acyl-CoA dehydrogenase, mitochondrial

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Macromolecule #2: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 4 / 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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 18616
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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