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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | human liver mitochondrial Aspartate aminotransferase | |||||||||
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![]() | human / liver / mitochondrial / Aspartate aminotransferase / TRANSFERASE | |||||||||
Function / homology | ![]() 4-hydroxyproline catabolic process / glutamate catabolic process to aspartate / glutamate catabolic process to 2-oxoglutarate / Degradation of cysteine and homocysteine / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / aspartate metabolic process / aspartate biosynthetic process / Aspartate and asparagine metabolism / glutamate metabolic process ...4-hydroxyproline catabolic process / glutamate catabolic process to aspartate / glutamate catabolic process to 2-oxoglutarate / Degradation of cysteine and homocysteine / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / aspartate metabolic process / aspartate biosynthetic process / Aspartate and asparagine metabolism / glutamate metabolic process / Glutamate and glutamine metabolism / aspartate catabolic process / 2-oxoglutarate metabolic process / aspartate transaminase / oxaloacetate metabolic process / 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 | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.99 Å | |||||||||
![]() | Zhang Z / Tringides M | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 51.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.4 KB 13.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.1 KB | Display | ![]() |
Images | ![]() | 97.8 KB | ||
Filedesc metadata | ![]() | 5.1 KB | ||
Others | ![]() ![]() | 95.3 MB 95.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 18.3 KB | Display | |
Data in CIF | ![]() | 23.4 KB | Display | |
Arichive directory | ![]() ![]() | 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 ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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
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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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Density Histograms |
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Sample components
-Entire : Aspartate aminotransferase
Entire | Name: Aspartate aminotransferase |
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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: ![]() |
-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: ![]() |
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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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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: ![]() |
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 |