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- EMDB-40466: human liver mitochondrial Short-chain specific acyl-CoA dehydrogenase -

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Basic information

Entry
Database: EMDB / ID: EMD-40466
Titlehuman liver mitochondrial Short-chain specific acyl-CoA dehydrogenase
Map data
Sample
  • Complex: Short-chain specific acyl-CoA dehydrogenase
    • Protein or peptide: Short-chain specific acyl-CoA dehydrogenase, mitochondrial
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: COENZYME A
Keywordshuman / liver / mitochondrial / Short-chain specific acyl-CoA dehydrogenase / OXIDOREDUCTASE
Function / homology
Function and homology information


butyrate catabolic process / Beta oxidation of butanoyl-CoA to acetyl-CoA / Beta oxidation of hexanoyl-CoA to butanoyl-CoA / short-chain acyl-CoA dehydrogenase / short-chain fatty acyl-CoA dehydrogenase activity / fatty acid beta-oxidation using acyl-CoA dehydrogenase / acyl-CoA dehydrogenase activity / fatty acid beta-oxidation / flavin adenine dinucleotide binding / mitochondrial matrix ...butyrate catabolic process / Beta oxidation of butanoyl-CoA to acetyl-CoA / Beta oxidation of hexanoyl-CoA to butanoyl-CoA / short-chain acyl-CoA dehydrogenase / short-chain fatty acyl-CoA dehydrogenase activity / fatty acid beta-oxidation using acyl-CoA dehydrogenase / acyl-CoA dehydrogenase activity / fatty acid beta-oxidation / flavin adenine dinucleotide binding / mitochondrial matrix / mitochondrion / nucleus
Similarity search - Function
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 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
Short-chain specific acyl-CoA dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 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 13, 2023-
Header (metadata) releaseFeb 21, 2024-
Map releaseFeb 21, 2024-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40466.png

Downloads & links

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Map

FileDownload / File: emd_40466.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8255 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.20164116 - 0.44647297
Average (Standard dev.)0.0016485327 (±0.013399159)
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: #2

Fileemd_40466_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_40466_half_map_2.map
Projections & Slices
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Sample components

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Entire : Short-chain specific acyl-CoA dehydrogenase

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

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

SupramoleculeName: Short-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: Short-chain specific acyl-CoA dehydrogenase, mitochondrial

MacromoleculeName: Short-chain specific acyl-CoA dehydrogenase, mitochondrial
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: short-chain acyl-CoA dehydrogenase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.346133 KDa
SequenceString: MAAALLARAS GPARRALCPR AWRQLHTIYQ SVELPETHQM LLQTCRDFAE KELFPIAAQV DKEHLFPAAQ VKKMGGLGLL AMDVPEELG GAGLDYLAYA IAMEEISRGC ASTGVIMSVN NSLYLGPILK FGSKEQKQAW VTPFTSGDKI GCFALSEPGN G SDAGAAST ...String:
MAAALLARAS GPARRALCPR AWRQLHTIYQ SVELPETHQM LLQTCRDFAE KELFPIAAQV DKEHLFPAAQ VKKMGGLGLL AMDVPEELG GAGLDYLAYA IAMEEISRGC ASTGVIMSVN NSLYLGPILK FGSKEQKQAW VTPFTSGDKI GCFALSEPGN G SDAGAAST TARAEGDSWV LNGTKAWITN AWEASAAVVF ASTDRALQNK GISAFLVPMP TPGLTLGKKE DKLGIRGSST AN LIFEDCR IPKDSILGEP GMGFKIAMQT LDMGRIGIAS QALGIAQTAL DCAVNYAENR MAFGAPLTKL QVIQFKLADM ALA LESARL LTWRAAMLKD NKKPFIKEAA MAKLAASEAA TAISHQAIQI LGGMGYVTEM PAERHYRDAR ITEIYEGTSE IQRL VIAGH LLRSYRS

UniProtKB: Short-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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Macromolecule #3: COENZYME A

MacromoleculeName: COENZYME A / type: ligand / ID: 3 / Number of copies: 4 / Formula: COA
Molecular weightTheoretical: 767.534 Da
Chemical component information

ChemComp-COA:
COENZYME A

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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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 16677
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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