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Yorodumi- EMDB-40466: human liver mitochondrial Short-chain specific acyl-CoA dehydrogenase -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40466 | |||||||||
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Title | human liver mitochondrial Short-chain specific acyl-CoA dehydrogenase | |||||||||
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Sample |
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Keywords | human / 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 / butyryl-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 / butyryl-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 / centrosome / mitochondrion / nucleoplasm / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.15 Å | |||||||||
Authors | Zhang Z | |||||||||
Funding support | United States, 1 items
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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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40466.map.gz | 83 MB | EMDB map data format | |
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Header (meta data) | emd-40466-v30.xml emd-40466.xml | 13.9 KB 13.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40466_fsc.xml | 13 KB | Display | FSC data file |
Images | emd_40466.png | 118.2 KB | ||
Filedesc metadata | emd-40466.cif.gz | 5.2 KB | ||
Others | emd_40466_half_map_1.map.gz emd_40466_half_map_2.map.gz | 154 MB 154 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40466 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40466 | HTTPS FTP |
-Related structure data
Related structure data | 8sgsMC 8sgpC 8sgrC 8sgvC 8shsC 8sk6C 8sk8C 8skrC 8sksC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_40466.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.8255 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_40466_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_40466_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Short-chain specific acyl-CoA dehydrogenase
Entire | Name: Short-chain specific acyl-CoA dehydrogenase |
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Components |
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-Supramolecule #1: Short-chain specific acyl-CoA dehydrogenase
Supramolecule | Name: Short-chain specific acyl-CoA dehydrogenase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Short-chain specific acyl-CoA dehydrogenase, mitochondrial
Macromolecule | Name: 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 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 44.346133 KDa |
Sequence | String: 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 |
-Macromolecule #2: FLAVIN-ADENINE DINUCLEOTIDE
Macromolecule | Name: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 4 / Formula: FAD |
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Molecular weight | Theoretical: 785.55 Da |
Chemical component information | ChemComp-FAD: |
-Macromolecule #3: COENZYME A
Macromolecule | Name: COENZYME A / type: ligand / ID: 3 / Number of copies: 4 / Formula: COA |
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Molecular weight | Theoretical: 767.534 Da |
Chemical component information | ChemComp-COA: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000 |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 35.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |