+Open data
-Basic information
Entry | Database: PDB / ID: 5zrv | ||||||
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Title | Structure of human mitochondrial trifunctional protein, octamer | ||||||
Components |
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Keywords | Liase / Oxidoreductase/Transferase / fatty acid beta-oxidation / cryo-EM single-particle reconstruction / mitochondrial trifunctional protein / Oxidoreductase-Transferase complex | ||||||
Function / homology | Function and homology information long-chain-3-hydroxyacyl-CoA dehydrogenase / Beta oxidation of myristoyl-CoA to lauroyl-CoA / cardiolipin acyl-chain remodeling / Acyl chain remodeling of CL / Beta oxidation of palmitoyl-CoA to myristoyl-CoA / acetyl-CoA C-myristoyltransferase / acetyl-CoA C-myristoyltransferase activity / mitochondrial fatty acid beta-oxidation multienzyme complex / mitochondrial fatty acid beta-oxidation of unsaturated fatty acids / 3-hydroxyacyl-CoA dehydratase activity ...long-chain-3-hydroxyacyl-CoA dehydrogenase / Beta oxidation of myristoyl-CoA to lauroyl-CoA / cardiolipin acyl-chain remodeling / Acyl chain remodeling of CL / Beta oxidation of palmitoyl-CoA to myristoyl-CoA / acetyl-CoA C-myristoyltransferase / acetyl-CoA C-myristoyltransferase activity / mitochondrial fatty acid beta-oxidation multienzyme complex / mitochondrial fatty acid beta-oxidation of unsaturated fatty acids / 3-hydroxyacyl-CoA dehydratase activity / Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA / Beta oxidation of hexanoyl-CoA to butanoyl-CoA / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / acetyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / long-chain-3-hydroxyacyl-CoA dehydrogenase activity / enoyl-CoA hydratase / acetyl-CoA C-acetyltransferase activity / 3-hydroxyacyl-CoA dehydrogenase activity / fatty-acyl-CoA binding / enoyl-CoA hydratase activity / mitochondrial envelope / lncRNA binding / fatty acid beta-oxidation / mitochondrial nucleoid / NAD+ binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to insulin / gene expression / mitochondrial inner membrane / cellular response to lipopolysaccharide / mitochondrial outer membrane / response to xenobiotic stimulus / protein-containing complex binding / endoplasmic reticulum / mitochondrion / RNA binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.7 Å | ||||||
Authors | Liang, K. / Li, N. / Dai, J. / Wang, X. / Liu, P. / Chen, X. / Wang, C. / Gao, N. / Xiao, J. | ||||||
Funding support | China, 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2018 Title: Cryo-EM structure of human mitochondrial trifunctional protein. Authors: Kai Liang / Ningning Li / Xiao Wang / Jianye Dai / Pulan Liu / Chu Wang / Xiao-Wei Chen / Ning Gao / Junyu Xiao / Abstract: The mitochondrial trifunctional protein (TFP) catalyzes three reactions in the fatty acid β-oxidation process. Mutations in the two TFP subunits cause mitochondrial trifunctional protein deficiency ...The mitochondrial trifunctional protein (TFP) catalyzes three reactions in the fatty acid β-oxidation process. Mutations in the two TFP subunits cause mitochondrial trifunctional protein deficiency and acute fatty liver of pregnancy that can lead to death. Here we report a 4.2-Å cryo-electron microscopy α2β2 tetrameric structure of the human TFP. The tetramer has a V-shaped architecture that displays a distinct assembly compared with the bacterial TFPs. A concave surface of the TFP tetramer interacts with the detergent molecules in the structure, suggesting that this region is involved in associating with the membrane. Deletion of a helical hairpin in TFPβ decreases its binding to the liposomes in vitro and reduces its membrane targeting in cells. Our results provide the structural basis for TFP function and have important implications for fatty acid oxidation related diseases. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5zrv.cif.gz | 561.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zrv.ent.gz | 366.8 KB | Display | PDB format |
PDBx/mmJSON format | 5zrv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/5zrv ftp://data.pdbj.org/pub/pdb/validation_reports/zr/5zrv | HTTPS FTP |
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-Related structure data
Related structure data | 6944MC 6940C 6945C 5zqzC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 83112.625 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HADHA, HADH / Production host: Escherichia coli (E. coli) References: UniProt: P40939, enoyl-CoA hydratase, long-chain-3-hydroxyacyl-CoA dehydrogenase #2: Protein | Mass: 51360.359 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HADHB, MSTP029 / Production host: Escherichia coli (E. coli) / References: UniProt: P55084, acetyl-CoA C-acyltransferase |
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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: human mitochondrial trifunctional protein / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Units: MEGADALTONS / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD |
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 FIELDBright-field microscopy |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.11.1_2575: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48564 / Details: Gold Standard / Symmetry type: POINT | ||||||||||||||||||||||||
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