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- EMDB-9071: Single-Molecule 3D Image of Human Plasma Intermediate-Density Lip... -

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Basic information

Database: EMDB / ID: EMD-9071
TitleSingle-Molecule 3D Image of Human Plasma Intermediate-Density Lipoprotein (No. 03)
Map data
SampleHuman plasma intermediate-density lipoprotein
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM / Resolution: 82.7 Å
AuthorsLei D / Yu Y / Kuang Y / Krauss R / Ren G
Funding support United States, 4 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DMR-1344290 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL115153 United States
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM104427 United States
CitationJournal: 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.
DepositionSep 3, 2018-
Header (metadata) releaseOct 31, 2018-
Map releaseJan 16, 2019-
UpdateDec 25, 2019-
Current statusDec 25, 2019Processing site: RCSB / Status: Released

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.008
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


FileDownload / File: emd_9071.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
2.4 Å/pix.
x 192 pix.
= 460.8 Å
2.4 Å/pix.
x 192 pix.
= 460.8 Å
2.4 Å/pix.
x 192 pix.
= 460.8 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.4 Å
Contour LevelMovie #1: 0.008
Minimum - Maximum-0.0018495909 - 0.016615853
Average (Standard dev.)0.0010565115 (±0.0029151184)
SymmetrySpace group: 1


Map geometry
Axis orderXYZ
CellA=B=C: 460.80002 Å
α=β=γ: 90.0 °

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
start NX/NY/NZ000
MAP C/R/S123
start NC/NR/NS-96-96-96
D min/max/mean-0.0020.0170.001

Supplemental data

Sample components

Entire Human plasma intermediate-density lipoprotein

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

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

Experimental details

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 %

Electron microscopy imaging

ImagingMicroscope: ZEISS LIBRA120PLUS
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 1.4 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)

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: 82.7 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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