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- EMDB-8044: Electron tomographic structure of an individual human plasma VLDL... -

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Basic information

Entry
Database: EMDB / ID: EMD-8044
TitleElectron tomographic structure of an individual human plasma VLDL particle (No.003)
Map datahuman plasma VLDL particle
Sample
  • Complex: Human Plasma Very-Low-Density Lipoprotein
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM / Resolution: 50.0 Å
AuthorsYu Y / Kuang Y / Lei D / Zhai X / Krauss R / Ren G
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM104427 United States
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
CitationJournal: J Lipid Res / Year: 2016
Title: Polyhedral 3D structure of human plasma very low density lipoproteins by individual particle cryo-electron tomography1.
Authors: Yadong Yu / Yu-Lin Kuang / Dongsheng Lei / Xiaobo Zhai / Meng Zhang / Ronald M Krauss / Gang Ren /
Abstract: Human VLDLs assembled in the liver and secreted into the circulation supply energy to peripheral tissues. VLDL lipolysis yields atherogenic LDLs and VLDL remnants that strongly correlate with CVD. ...Human VLDLs assembled in the liver and secreted into the circulation supply energy to peripheral tissues. VLDL lipolysis yields atherogenic LDLs and VLDL remnants that strongly correlate with CVD. Although the composition of VLDL particles has been well-characterized, their 3D structure is elusive because of their variations in size, heterogeneity in composition, structural flexibility, and mobility in solution. Here, we employed cryo-electron microscopy and individual-particle electron tomography to study the 3D structure of individual VLDL particles (without averaging) at both below and above their lipid phase transition temperatures. The 3D reconstructions of VLDL and VLDL bound to antibodies revealed an unexpected polyhedral shape, in contrast to the generally accepted model of a spherical emulsion-like particle. The smaller curvature of surface lipids compared with HDL may also reduce surface hydrophobicity, resulting in lower binding affinity to the hydrophobic distal end of the N-terminal β-barrel domain of cholesteryl ester transfer protein (CETP) compared with HDL. The directional binding of CETP to HDL and VLDL may explain the function of CETP in transferring TGs and cholesteryl esters between these particles. This first visualization of the 3D structure of VLDL could improve our understanding of the role of VLDL in atherogenesis.
History
DepositionJan 14, 2016-
Header (metadata) releaseJul 13, 2016-
Map releaseNov 2, 2016-
UpdateJan 29, 2020-
Current statusJan 29, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0334
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0334
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8044.png

Downloads & links

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Map

FileDownload / File: emd_8044.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhuman plasma VLDL particle
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.4 Å/pix.
x 200 pix.
= 480. Å		2.4 Å/pix.
x 200 pix.
= 480. Å		2.4 Å/pix.
x 200 pix.
= 480. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelMovie #1: 0.0334
Minimum - Maximum-0.045099497 - 0.100072175
Average (Standard dev.)0.0009784028 (±0.022077363)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions200200200
Spacing200200200
CellA=B=C: 480.00003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.42.42.4
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z480.000480.000480.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-38-19-20
NX/NY/NZ858082
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200200
D min/max/mean-0.0450.1000.001

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Supplemental data

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Sample components

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Entire : Human Plasma Very-Low-Density Lipoprotein

EntireName: Human Plasma Very-Low-Density Lipoprotein
Components
  • Complex: Human Plasma Very-Low-Density Lipoprotein

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Supramolecule #1: Human Plasma Very-Low-Density Lipoprotein

SupramoleculeName: Human Plasma Very-Low-Density Lipoprotein / type: complex / ID: 1 / Parent: 0
Details: VLDL isolated from human plasma by density gradient centrifugation.
Source (natural)Organism: Homo sapiens (human) / Tissue: blood
Molecular weightExperimental: 8.0 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

Concentration0.4 mg/mL
BufferpH: 7.3
Component:
ConcentrationFormulaName
8.0 mg/mLNaClsodium chloride
0.2 mg/mLKClpotassium chloride
1.15 mg/mLNa2HPO4Sodium Phosphate, dibasic
0.2 mg/mLKH2PO4Potassium Phosphate, monobasic

Details: DPBS
GridModel: EMS Lacey carbon / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: LACEY / Support film - Film thickness: 50.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: LEICA EM GP
Details: 3 microliter of specimen blotted for 3 seconds before plunging.
DetailsThis sample was monodisperse.
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeZEISS LIBRA120PLUS
TemperatureMin: 90.0 K / Max: 93.0 K
Specialist opticsEnergy filter - Name: Zeiss in-column Omega / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 15.0 µm / Number grids imaged: 1 / Number real images: 85 / Average exposure time: 0.5 sec. / Average electron dose: 1.8 e/Å2
Details: Images were collected by using the Gatan Tomography module of Digital Micrograph. XY tracking and focusing were done manually.
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsC2 aperture diameter: 75.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 1.5 µm / Calibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN

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Image processing

DetailsDefects in images such as bad pixels and X-rays were removed prior to alignment and 3D reconstruction.
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 50.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IPET
Details: The 3D reconstruction was conducted by using Individual Particle Electron Tomography (IPET)
Number images used: 85
CTF correctionSoftware - Name: TOMOCTF (ver. V. October 2012)

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