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Open data
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Basic information
Entry | Database: PDB / ID: 8eoj | ||||||
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Title | Microsomal triglyceride transfer protein | ||||||
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![]() | TRANSPORT PROTEIN / Microsomal triglyceride transfer protein / human liver / LIPID TRANSPORT / ISOMERASE | ||||||
Function / homology | ![]() plasma lipoprotein particle assembly / triglyceride transfer activity / chylomicron assembly / phosphatidylcholine transfer activity / regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / procollagen-proline 4-dioxygenase complex / interleukin-23-mediated signaling pathway / VLDL assembly / insulin processing / triglyceride transport ...plasma lipoprotein particle assembly / triglyceride transfer activity / chylomicron assembly / phosphatidylcholine transfer activity / regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / procollagen-proline 4-dioxygenase complex / interleukin-23-mediated signaling pathway / VLDL assembly / insulin processing / triglyceride transport / phosphatidylethanolamine transfer activity / phospholipid transfer activity / LDL remodeling / procollagen-proline 4-dioxygenase activity / thiol oxidase activity / protein disulfide-isomerase / ceramide 1-phosphate transfer activity / peptidyl-proline hydroxylation to 4-hydroxy-L-proline / very-low-density lipoprotein particle assembly / phospholipid transporter activity / endoplasmic reticulum chaperone complex / Collagen biosynthesis and modifying enzymes / protein folding in endoplasmic reticulum / lipid transporter activity / Chylomicron assembly / lipoprotein metabolic process / phospholipid transport / cholesterol transfer activity / Interleukin-23 signaling / interleukin-12-mediated signaling pathway / low-density lipoprotein particle remodeling / cellular response to interleukin-7 / Interleukin-12 signaling / lipoprotein transport / microvillus membrane / triglyceride metabolic process / protein disulfide isomerase activity / Insulin processing / Detoxification of Reactive Oxygen Species / apolipoprotein binding / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of cell adhesion / protein secretion / protein-disulfide reductase activity / endoplasmic reticulum to Golgi vesicle-mediated transport / positive regulation of substrate adhesion-dependent cell spreading / response to endoplasmic reticulum stress / establishment of localization in cell / cholesterol homeostasis / brush border membrane / Hedgehog ligand biogenesis / Post-translational protein phosphorylation / lipid metabolic process / response to calcium ion / circadian rhythm / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / melanosome / integrin binding / protein folding / lamellipodium / actin binding / cellular response to hypoxia / basolateral plasma membrane / vesicle / positive regulation of viral entry into host cell / cytoskeleton / receptor complex / protein heterodimerization activity / endoplasmic reticulum lumen / external side of plasma membrane / focal adhesion / lipid binding / protein-containing complex binding / Golgi apparatus / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / extracellular exosome / extracellular region / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.07 Å | ||||||
![]() | Zhang, Z. | ||||||
Funding support | ![]()
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![]() | ![]() Title: High-resolution structural-omics of human liver enzymes. Authors: Chih-Chia Su / Meinan Lyu / Zhemin Zhang / Masaru Miyagi / Wei Huang / Derek J Taylor / Edward W Yu / ![]() Abstract: We applied raw human liver microsome lysate to a holey carbon grid and used cryo-electron microscopy (cryo-EM) to define its composition. From this sample we identified and simultaneously determined ...We applied raw human liver microsome lysate to a holey carbon grid and used cryo-electron microscopy (cryo-EM) to define its composition. From this sample we identified and simultaneously determined high-resolution structural information for ten unique human liver enzymes involved in diverse cellular processes. Notably, we determined the structure of the endoplasmic bifunctional protein H6PD, where the N- and C-terminal domains independently possess glucose-6-phosphate dehydrogenase and 6-phosphogluconolactonase enzymatic activity, respectively. We also obtained the structure of heterodimeric human GANAB, an ER glycoprotein quality-control machinery that contains a catalytic α subunit and a noncatalytic β subunit. In addition, we observed a decameric peroxidase, PRDX4, which directly contacts a disulfide isomerase-related protein, ERp46. Structural data suggest that several glycosylations, bound endogenous compounds, and ions associate with these human liver enzymes. These results highlight the importance of cryo-EM in facilitating the elucidation of human organ proteomics at the atomic level. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 244.7 KB | Display | ![]() |
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PDB format | ![]() | 191.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 48.6 KB | Display | |
Data in CIF | ![]() | 71.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 23426 ![]() 28377MC ![]() 7uzmC ![]() 8ekwC ![]() 8ekyC ![]() 8em2C ![]() 8emrC ![]() 8emsC ![]() 8emtC ![]() 8eneC ![]() 8eorC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 57190.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Protein | Mass: 99474.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Microsomal triglyceride transfer protein / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 3291 nm / Nominal defocus min: 170 nm |
Image recording | Electron dose: 41.25 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 487553 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 249877 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.46 Å2 | ||||||||||||||||||||||||
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