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- EMDB-9079: Single-Molecule 3D Image of Human Plasma Intermediate-Density Lip... -

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Basic information

Entry
Database: EMDB / ID: 9079
TitleSingle-Molecule 3D Image of Human Plasma Intermediate-Density Lipoprotein (No. 11)
Map data
SampleHuman plasma intermediate-density lipoprotein:
SourceHomo sapiens (human)
Methodelectron tomography / cryo EM / 68.8 Å resolution
AuthorsLei D / Yu Y / Kuang Y / Krauss R / Ren G
CitationJournal: Biochim Biophys Acta Mol Cell Biol Lipids / Year: 2018
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.
DateDeposition: Sep 3, 2018 / Header (metadata) release: Oct 31, 2018 / Map release: Jan 2, 2019 / Last update: Jan 2, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9079.map.gz (map file in CCP4 format, 28312 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
192 pix
2.4 Å/pix.
= 460.8 Å
192 pix
2.4 Å/pix.
= 460.8 Å
192 pix
2.4 Å/pix.
= 460.8 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.4 Å
Density
Contour Level:0.1 (movie #1):
Minimum - Maximum-0.061421104 - 0.36397576
Average (Standard dev.)0.015196882 (0.05394202)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions192192192
Origin-96.0-96.0-96.0
Limit95.095.095.0
Spacing192192192
CellA=B=C: 460.80002 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.42.42.4
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z460.800460.800460.800
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-96-96-96
NC/NR/NS192192192
D min/max/mean-0.0610.3640.015

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Supplemental data

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Sample components

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Entire Human plasma intermediate-density lipoprotein

EntireName: Human plasma intermediate-density lipoprotein / Number of components: 1

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Component #1: cellular-component, Human plasma intermediate-density lipoprotein

Cellular-componentName: Human plasma intermediate-density lipoprotein / Recombinant expression: No
MassExperimental: 3 MDa
SourceSpecies: Homo sapiens (human)
Source (natural)Organ or tissue: Blood

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 2 mg/ml
Buffer solution: Dulbecco's phosphate buffered saline (DPBS)
pH: 7
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 80 %

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Electron microscopy imaging

ImagingMicroscope: ZEISS LIBRA120PLUS
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 1.39 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000.0 X (nominal) / Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Energy filter: In-column Omega Filter
Specimen HolderModel: OTHER
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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Image processing

ProcessingMethod: electron tomography / Number of sections: 35
Details: X-ray speckles in images were removed before CTF correction.
3D reconstructionAlgorithm: FOURIER SPACE / Resolution: 68.8 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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