+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40565 | |||||||||
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Title | human liver mitochondrial Aspartate aminotransferase | |||||||||
Map data | ||||||||||
Sample |
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Keywords | human / liver / mitochondrial / Aspartate aminotransferase / TRANSFERASE | |||||||||
Function / homology | Function and homology information 4-hydroxyproline catabolic process / glutamate catabolic process to aspartate / glutamate catabolic process to 2-oxoglutarate / aspartate biosynthetic process / Degradation of cysteine and homocysteine / aspartate catabolic process / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / aspartate metabolic process / glutamate metabolic process ...4-hydroxyproline catabolic process / glutamate catabolic process to aspartate / glutamate catabolic process to 2-oxoglutarate / aspartate biosynthetic process / Degradation of cysteine and homocysteine / aspartate catabolic process / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / aspartate metabolic process / glutamate metabolic process / Aspartate and asparagine metabolism / Glutamate and glutamine metabolism / 2-oxoglutarate metabolic process / oxaloacetate metabolic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / Glyoxylate metabolism and glycine degradation / Gluconeogenesis / fatty acid transport / pyridoxal phosphate binding / response to ethanol / mitochondrial matrix / mitochondrion / RNA binding / extracellular exosome / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.99 Å | |||||||||
Authors | Zhang Z / Tringides M | |||||||||
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_40565.map.gz | 51.2 MB | EMDB map data format | |
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Header (meta data) | emd-40565-v30.xml emd-40565.xml | 13.4 KB 13.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40565_fsc.xml | 11.1 KB | Display | FSC data file |
Images | emd_40565.png | 97.8 KB | ||
Filedesc metadata | emd-40565.cif.gz | 5.1 KB | ||
Others | emd_40565_half_map_1.map.gz emd_40565_half_map_2.map.gz | 95.3 MB 95.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40565 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40565 | HTTPS FTP |
-Related structure data
Related structure data | 8skrMC 8sgpC 8sgrC 8sgsC 8sgvC 8shsC 8sk6C 8sk8C 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_40565.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.825 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_40565_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_40565_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Aspartate aminotransferase
Entire | Name: Aspartate aminotransferaseAspartate transaminase |
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Components |
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-Supramolecule #1: Aspartate aminotransferase
Supramolecule | Name: Aspartate aminotransferase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Aspartate aminotransferase, mitochondrial
Macromolecule | Name: Aspartate aminotransferase, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: aspartate transaminase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 47.580578 KDa |
Sequence | String: MALLHSGRVL PGIAAAFHPG LAAAASARAS SWWTHVEMGP PDPILGVTEA FKRDTNSKKM NLGVGAYRDD NGKPYVLPSV RKAEAQIAA KNLDKEYLPI GGLAEFCKAS AELALGENSE VLKSGRFVTV QTISGTGALR IGASFLQRFF KFSRDVFLPK P TWGNHTPI ...String: MALLHSGRVL PGIAAAFHPG LAAAASARAS SWWTHVEMGP PDPILGVTEA FKRDTNSKKM NLGVGAYRDD NGKPYVLPSV RKAEAQIAA KNLDKEYLPI GGLAEFCKAS AELALGENSE VLKSGRFVTV QTISGTGALR IGASFLQRFF KFSRDVFLPK P TWGNHTPI FRDAGMQLQG YRYYDPKTCG FDFTGAVEDI SKIPEQSVLL LHACAHNPTG VDPRPEQWKE IATVVKKRNL FA FFDMAYQ GFASGDGDKD AWAVRHFIEQ GINVCLCQSY AKNMGLYGER VGAFTMVCKD ADEAKRVESQ LKILIRPMYS NPP LNGARI AAAILNTPDL RKQWLQEVKV MADRIIGMRT QLVSNLKKEG STHNWQHITD QIGMFCFTGL KPEQVERLIK EFSI YMTKD GRISVAGVTS SNVGYLAHAI HQVTK UniProtKB: Aspartate aminotransferase, mitochondrial |
-Macromolecule #2: PYRIDOXAL-5'-PHOSPHATE
Macromolecule | Name: PYRIDOXAL-5'-PHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: PLP |
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Molecular weight | Theoretical: 247.142 Da |
Chemical component information | ChemComp-PLP: |
-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 |