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- EMDB-40493: human liver mitochondrial Aldehyde dehydrogenase ALDH2 -

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Basic information

Entry
Database: EMDB / ID: EMD-40493
Titlehuman liver mitochondrial Aldehyde dehydrogenase ALDH2
Map data
Sample
  • Complex: ALDH2
    • Protein or peptide: Aldehyde dehydrogenase, mitochondrial
Keywordshuman / liver / mitochondrial / Aldehyde dehydrogenase / ALDH2 / OXIDOREDUCTASE
Function / homology
Function and homology information


Metabolism of serotonin / : / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / phenylacetaldehyde dehydrogenase (NAD+) activity / aldehyde catabolic process / alcohol metabolic process / ethanol catabolic process / aldehyde dehydrogenase [NAD(P)+] activity / Ethanol oxidation ...Metabolism of serotonin / : / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / phenylacetaldehyde dehydrogenase (NAD+) activity / aldehyde catabolic process / alcohol metabolic process / ethanol catabolic process / aldehyde dehydrogenase [NAD(P)+] activity / Ethanol oxidation / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / carboxylesterase activity / aldehyde dehydrogenase (NAD+) activity / Smooth Muscle Contraction / Mitochondrial protein degradation / NAD binding / carbohydrate metabolic process / electron transfer activity / mitochondrial matrix / mitochondrion / extracellular exosome
Similarity search - Function
Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
Aldehyde dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.66 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 14, 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_40493.png

Downloads & links

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Map

FileDownload / File: emd_40493.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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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-0.23779692 - 0.5625596
Average (Standard dev.)0.0012718203 (±0.013840464)
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_40493_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_40493_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : ALDH2

EntireName: ALDH2
Components
  • Complex: ALDH2
    • Protein or peptide: Aldehyde dehydrogenase, mitochondrial

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Supramolecule #1: ALDH2

SupramoleculeName: ALDH2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Aldehyde dehydrogenase, mitochondrial

MacromoleculeName: Aldehyde dehydrogenase, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: aldehyde dehydrogenase (NAD+)
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.441047 KDa
SequenceString: MLRAAARFGP RLGRRLLSAA ATQAVPAPNQ QPEVFCNQIF INNEWHDAVS RKTFPTVNPS TGEVICQVAE GDKEDVDKAV KAARAAFQL GSPWRRMDAS HRGRLLNRLA DLIERDRTYL AALETLDNGK PYVISYLVDL DMVLKCLRYY AGWADKYHGK T IPIDGDFF ...String:
MLRAAARFGP RLGRRLLSAA ATQAVPAPNQ QPEVFCNQIF INNEWHDAVS RKTFPTVNPS TGEVICQVAE GDKEDVDKAV KAARAAFQL GSPWRRMDAS HRGRLLNRLA DLIERDRTYL AALETLDNGK PYVISYLVDL DMVLKCLRYY AGWADKYHGK T IPIDGDFF SYTRHEPVGV CGQIIPWNFP LLMQAWKLGP ALATGNVVVM KVAEQTPLTA LYVANLIKEA GFPPGVVNIV PG FGPTAGA AIASHEDVDK VAFTGSTEIG RVIQVAAGSS NLKRVTLELG GKSPNIIMSD ADMDWAVEQA HFALFFNQGQ CCC AGSRTF VQEDIYDEFV ERSVARAKSR VVGNPFDSKT EQGPQVDETQ FKKILGYINT GKQEGAKLLC GGGIAADRGY FIQP TVFGD VQDGMTIAKE EIFGPVMQIL KFKTIEEVVG RANNSTYGLA AAVFTKDLDK ANYLSQALQA GTVWVNCYDV FGAQS PFGG YKMSGSGREL GEYGLQAYTE VKTVTVKVPQ KNS

UniProtKB: Aldehyde dehydrogenase, 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: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 82360
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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