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- EMDB-40556: human liver mitochondrial Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase -

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Basic information

Entry
Database: EMDB / ID: EMD-40556
Titlehuman liver mitochondrial Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase
Map data
Sample
  • Complex: Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase
    • Protein or peptide: Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial
Keywordshuman / liver / mitochondrial / Delta(3 / 5)-Delta(2 / 4)-dienoyl-CoA isomerase / ISOMERASE
Function / homology
Function and homology information


delta(3,5)-delta(2,4)-dienoyl-CoA isomerase activity / Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / fatty acid beta-oxidation / peroxisomal matrix / Mitochondrial protein degradation / Peroxisomal protein import / peroxisome / mitochondrial matrix / mitochondrion / extracellular exosome ...delta(3,5)-delta(2,4)-dienoyl-CoA isomerase activity / Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / fatty acid beta-oxidation / peroxisomal matrix / Mitochondrial protein degradation / Peroxisomal protein import / peroxisome / mitochondrial matrix / mitochondrion / extracellular exosome / membrane / cytosol
Similarity search - Function
Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase Ech1-like / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsZhang Z / Tringides M
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 18, 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_40556.png

Downloads & links

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Map

FileDownload / File: emd_40556.map.gz / Format: CCP4 / Size: 125 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 320 pix.
= 264. Å		0.83 Å/pix.
x 320 pix.
= 264. Å		0.83 Å/pix.
x 320 pix.
= 264. Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.193269 - 0.4402479
Average (Standard dev.)0.00035076024 (±0.015334547)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_40556_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_40556_half_map_2.map
Projections & Slices
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Sample components

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Entire : Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase

EntireName: Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase
Components
  • Complex: Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase
    • Protein or peptide: Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial

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Supramolecule #1: Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase

SupramoleculeName: Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial

MacromoleculeName: Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial
type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
EC number: Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.859137 KDa
SequenceString: MAAGIVASRR LRDLLTRRLT GSNYPGLSIS LRLTGSSAQE EASGVALGEA PDHSYESLRV TSAQKHVLHV QLNRPNKRNA MNKVFWREM VECFNKISRD ADCRAVVISG AGKMFTAGID LMDMASDILQ PKGDDVARIS WYLRDIITRY QETFNVIERC P KPVIAAVH ...String:
MAAGIVASRR LRDLLTRRLT GSNYPGLSIS LRLTGSSAQE EASGVALGEA PDHSYESLRV TSAQKHVLHV QLNRPNKRNA MNKVFWREM VECFNKISRD ADCRAVVISG AGKMFTAGID LMDMASDILQ PKGDDVARIS WYLRDIITRY QETFNVIERC P KPVIAAVH GGCIGGGVDL VTACDIRYCA QDAFFQVKEV DVGLAADVGT LQRLPKVIGN QSLVNELAFT ARKMMADEAL GS GLVSRVF PDKEVMLDAA LALAAEISSK SPVAVQSTKV NLLYSRDHSV AESLNYVASW NMSMLQTQDL VKSVQATTEN KEL KTVTFS KL

UniProtKB: Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase, mitochondrial

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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: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8862
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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