+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40493 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | human liver mitochondrial Aldehyde dehydrogenase ALDH2 | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | human / 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 / aldehyde catabolic process / phenylacetaldehyde dehydrogenase (NAD+) activity / alcohol metabolic process / aldehyde dehydrogenase [NAD(P)+] activity / ethanol catabolic process / Ethanol oxidation ...Metabolism of serotonin / : / regulation of dopamine biosynthetic process / regulation of serotonin biosynthetic process / aldehyde catabolic process / phenylacetaldehyde dehydrogenase (NAD+) activity / alcohol metabolic process / aldehyde dehydrogenase [NAD(P)+] activity / ethanol catabolic process / Ethanol oxidation / carboxylesterase activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / 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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.66 Å | |||||||||
Authors | Zhang Z | |||||||||
Funding support | United States, 1 items
| |||||||||
Citation | Journal: 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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_40493.map.gz | 83.3 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-40493-v30.xml emd-40493.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40493_fsc.xml | 12.9 KB | Display | FSC data file |
Images | emd_40493.png | 105.1 KB | ||
Filedesc metadata | emd-40493.cif.gz | 5.1 KB | ||
Others | emd_40493_half_map_1.map.gz emd_40493_half_map_2.map.gz | 154.2 MB 154.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40493 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40493 | HTTPS FTP |
-Validation report
Summary document | emd_40493_validation.pdf.gz | 894.8 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_40493_full_validation.pdf.gz | 894.3 KB | Display | |
Data in XML | emd_40493_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | emd_40493_validation.cif.gz | 26.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40493 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40493 | HTTPS FTP |
-Related structure data
Related structure data | 8shsMC 8sgpC 8sgrC 8sgsC 8sgvC 8sk6C 8sk8C 8skrC 8sksC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_40493.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 0.8255 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #2
File | emd_40493_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_40493_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : ALDH2
Entire | Name: ALDH2 |
---|---|
Components |
|
-Supramolecule #1: ALDH2
Supramolecule | Name: ALDH2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Aldehyde dehydrogenase, mitochondrial
Macromolecule | Name: 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 weight | Theoretical: 56.441047 KDa |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 35.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |