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Yorodumi- PDB-8sgs: human liver mitochondrial Short-chain specific acyl-CoA dehydrogenase -
+Open data
-Basic information
Entry | Database: PDB / ID: 8sgs | ||||||
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Title | human liver mitochondrial Short-chain specific acyl-CoA dehydrogenase | ||||||
Components | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / human / liver / mitochondrial / Short-chain specific acyl-CoA dehydrogenase | ||||||
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 / : / 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 / : / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 Å | ||||||
Authors | Zhang, Z. | ||||||
Funding support | United States, 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8sgs.cif.gz | 290 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8sgs.ent.gz | 235.4 KB | Display | PDB format |
PDBx/mmJSON format | 8sgs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8sgs_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 8sgs_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 8sgs_validation.xml.gz | 62.9 KB | Display | |
Data in CIF | 8sgs_validation.cif.gz | 87.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sg/8sgs ftp://data.pdbj.org/pub/pdb/validation_reports/sg/8sgs | HTTPS FTP |
-Related structure data
Related structure data | 40466MC 8sgpC 8sgrC 8sgvC 8shsC 8sk6C 8sk8C 8skrC 8sksC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 44346.133 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) References: UniProt: P16219, short-chain acyl-CoA dehydrogenase #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-COA / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Short-chain specific acyl-CoA dehydrogenase / Type: COMPLEX / Entity ID: #1 / Source: NATURAL |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 35 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16677 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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