Journal: Biochim Biophys Acta Mol Cell Biol Lipids / Year: 2019 Title: Single-molecule 3D imaging of human plasma intermediate-density lipoproteins reveals a polyhedral structure. Authors: Dongsheng Lei / Yadong Yu / Yu-Lin Kuang / Jianfang Liu / Ronald M Krauss / Gang Ren Abstract: Intermediate-density lipoproteins (IDLs), the remnants of very-low-density lipoproteins via lipolysis, are rich in cholesteryl ester and are associated with cardiovascular disease. Despite ...Intermediate-density lipoproteins (IDLs), the remnants of very-low-density lipoproteins via lipolysis, are rich in cholesteryl ester and are associated with cardiovascular disease. Despite pharmacological interest in IDLs, their three-dimensional (3D) structure is still undetermined due to their variation in size, composition, and dynamic structure. To explore the 3D structure of IDLs, we reconstructed 3D density maps from individual IDL particles using cryo-electron microscopy (cryo-EM) and individual-particle electron tomography (IPET, without averaging from different molecules). 3D reconstructions of IDLs revealed an unexpected polyhedral structure that deviates from the generally assumed spherical shape model (Frias et al., 2007; Olson, 1998; Shen et al., 1977). The polyhedral-shaped IDL contains a high-density shell formed by flat surfaces that are similar to those of very-low-density lipoproteins but have sharper dihedral angles between nearby surfaces. These flat surfaces would be less hydrophobic than the curved surface of mature spherical high-density lipoprotein (HDL), leading to a lower binding affinity of IDL to hydrophobic proteins (such as cholesteryl ester transfer protein) than HDL. This is the first visualization of the IDL 3D structure, which could provide fundamental clues for delineating the role of IDL in lipid metabolism and cardiovascular disease.
Date
Deposition: Sep 3, 2018 / Header (metadata) release: Oct 31, 2018 / Map release: Jan 16, 2019 / Last update: Jan 16, 2019
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Structure visualization
Movie
Surface view with section colored by density value
Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 80 %
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Electron microscopy imaging
Imaging
Microscope: ZEISS LIBRA120PLUS
Electron gun
Electron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 1.45 e/Å2 / Illumination mode: FLOOD BEAM
Lens
Magnification: 50000.0 X (nominal) / Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Energy filter: In-column Omega Filter
Specimen Holder
Model: OTHER
Camera
Detector: GATAN ULTRASCAN 4000 (4k x 4k)
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Image processing
Processing
Method: electron tomography / Number of sections: 35 Details: X-ray speckles in images were removed before CTF correction.
3D reconstruction
Algorithm: FOURIER SPACE / Resolution: 96.1 Å / Resolution method: FSC 0.5 CUT-OFF Details: The 3D reconstruction was performed by using individual-particle electron tomography (IPET). The obtained 3D map was low-pass filtered to 8 nm.
FSC plot (resolution estimation)
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