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- EMDB-40465: human liver mitochondrial Isovaleryl-CoA dehydrogenase -

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Basic information

Entry
Database: EMDB / ID: EMD-40465
Titlehuman liver mitochondrial Isovaleryl-CoA dehydrogenase
Map data
Sample
  • Complex: Isovaleryl-CoA dehydrogenase
    • Protein or peptide: Isovaleryl-CoA dehydrogenase, mitochondrial
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
Keywordshuman / liver / mitochondrial / Isovaleryl-CoA dehydrogenase / OXIDOREDUCTASE
Function / homology
Function and homology information


Isovaleric acidemia / isovaleryl-CoA dehydrogenase / 3-methylbutanoyl-CoA dehydrogenase activity / short-chain acyl-CoA dehydrogenase / L-leucine catabolic process / fatty acid beta-oxidation using acyl-CoA dehydrogenase / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / flavin adenine dinucleotide binding / mitochondrial matrix ...Isovaleric acidemia / isovaleryl-CoA dehydrogenase / 3-methylbutanoyl-CoA dehydrogenase activity / short-chain acyl-CoA dehydrogenase / L-leucine catabolic process / fatty acid beta-oxidation using acyl-CoA dehydrogenase / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / flavin adenine dinucleotide binding / mitochondrial matrix / mitochondrion / nucleoplasm / identical protein binding
Similarity search - Function
Isovaleryl-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 ...Isovaleryl-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
Isovaleryl-CoA dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 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_40465.png

Downloads & links

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Map

FileDownload / File: emd_40465.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

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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-0.31448048 - 0.66026866
Average (Standard dev.)0.0019333798 (±0.020140827)
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_40465_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: #2

Fileemd_40465_half_map_2.map
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Sample components

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Entire : Isovaleryl-CoA dehydrogenase

EntireName: Isovaleryl-CoA dehydrogenase
Components
  • Complex: Isovaleryl-CoA dehydrogenase
    • Protein or peptide: Isovaleryl-CoA dehydrogenase, mitochondrial
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE

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Supramolecule #1: Isovaleryl-CoA dehydrogenase

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

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Macromolecule #1: Isovaleryl-CoA dehydrogenase, mitochondrial

MacromoleculeName: Isovaleryl-CoA dehydrogenase, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: isovaleryl-CoA dehydrogenase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.707703 KDa
SequenceString: MAEMATATRL LGWRVASWRL RPPLAGFVSQ RAHSLLPVDD AINGLSEEQR QLRQTMAKFL QEHLAPKAQE IDRSNEFKNL REFWKQLGN LGVLGITAPV QYGGSGLGYL EHVLVMEEIS RASGAVGLSY GAHSNLCINQ LVRNGNEAQK EKYLPKLISG E YIGALAMS ...String:
MAEMATATRL LGWRVASWRL RPPLAGFVSQ RAHSLLPVDD AINGLSEEQR QLRQTMAKFL QEHLAPKAQE IDRSNEFKNL REFWKQLGN LGVLGITAPV QYGGSGLGYL EHVLVMEEIS RASGAVGLSY GAHSNLCINQ LVRNGNEAQK EKYLPKLISG E YIGALAMS EPNAGSDVVS MKLKAEKKGN HYILNGNKFW ITNGPDADVL IVYAKTDLAA VPASRGITAF IVEKGMPGFS TS KKLDKLG MRGSNTCELI FEDCKIPAAN ILGHENKGVY VLMSGLDLER LVLAGGPLGL MQAVLDHTIP YLHVREAFGQ KIG HFQLMQ GKMADMYTRL MACRQYVYNV AKACDEGHCT AKDCAGVILY SAECATQVAL DGIQCFGGNG YINDFPMGRF LRDA KLYEI GAGTSEVRRL VIGRAFNADF H

UniProtKB: Isovaleryl-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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 13185
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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