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- EMDB-40565: human liver mitochondrial Aspartate aminotransferase -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-40565
Titlehuman liver mitochondrial Aspartate aminotransferase
Map data
Sample
  • Complex: Aspartate aminotransferase
    • Protein or peptide: Aspartate aminotransferase, mitochondrial
  • Ligand: PYRIDOXAL-5'-PHOSPHATE
Keywordshuman / liver / mitochondrial / Aspartate aminotransferase / TRANSFERASE
Function / homology
Function and homology information


trans-4-hydroxy-L-proline catabolic process / Malate-aspartate shuttle / L-glutamate catabolic process to aspartate / aspartate biosynthetic process / malate-aspartate shuttle / L-aspartate catabolic process / Degradation of cysteine and homocysteine / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / aspartate metabolic process ...trans-4-hydroxy-L-proline catabolic process / Malate-aspartate shuttle / L-glutamate catabolic process to aspartate / aspartate biosynthetic process / malate-aspartate shuttle / L-aspartate catabolic process / Degradation of cysteine and homocysteine / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / aspartate metabolic process / Glyoxylate metabolism and glycine degradation / glutamate metabolic process / Aspartate and asparagine metabolism / Glutamate and glutamine metabolism / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / oxaloacetate metabolic process / 2-oxoglutarate metabolic process / fatty acid transport / pyridoxal phosphate binding / response to ethanol / mitochondrial matrix / mitochondrion / RNA binding / extracellular exosome / plasma membrane
Similarity search - Function
Aspartate/other aminotransferase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Aspartate aminotransferase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.99 Å
AuthorsZhang Z / Tringides M
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 20, 2023-
Header (metadata) releaseFeb 21, 2024-
Map releaseFeb 21, 2024-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40565.png

Downloads & links

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Map

FileDownload / File: emd_40565.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 247.5 Å		0.83 Å/pix.
x 300 pix.
= 247.5 Å		0.83 Å/pix.
x 300 pix.
= 247.5 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.31546015 - 0.621514
Average (Standard dev.)-0.0006728058 (±0.017014833)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 247.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_40565_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_40565_half_map_2.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Aspartate aminotransferase

EntireName: Aspartate aminotransferase
Components
  • Complex: Aspartate aminotransferase
    • Protein or peptide: Aspartate aminotransferase, mitochondrial
  • Ligand: PYRIDOXAL-5'-PHOSPHATE

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Supramolecule #1: Aspartate aminotransferase

SupramoleculeName: Aspartate aminotransferase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Aspartate aminotransferase, mitochondrial

MacromoleculeName: Aspartate aminotransferase, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: aspartate transaminase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.580578 KDa
SequenceString: 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

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Macromolecule #2: PYRIDOXAL-5'-PHOSPHATE

MacromoleculeName: PYRIDOXAL-5'-PHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: PLP
Molecular weightTheoretical: 247.142 Da
Chemical component information

ChemComp-PLP:
PYRIDOXAL-5'-PHOSPHATE

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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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15723
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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