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- EMDB-8051: Electron tomographic structure of a human plasma VLDL particle in... -

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Basic information

Entry
Database: EMDB / ID: EMD-8051
TitleElectron tomographic structure of a human plasma VLDL particle in complex with monoclonal antibody mAB012 (No.004)
Map datahuman plasma VLDL particle in complex with monoclonal antibody mAB012
Sample
  • Complex: VLDL in complex with antibody mAB012Very low-density lipoprotein
    • Complex: human plasma VLDL
    • Complex: Monoclonal IgG antibody mAB012
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodelectron tomography / cryo EM / Resolution: 80.0 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: 0.0306
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0306
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8051.png

Downloads & links

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Map

FileDownload / File: emd_8051.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhuman plasma VLDL particle in complex with monoclonal antibody mAB012
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.8 Å/pix.
x 160 pix.
= 768. Å		4.8 Å/pix.
x 160 pix.
= 768. Å		4.8 Å/pix.
x 160 pix.
= 768. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelMovie #1: 0.0306
Minimum - Maximum-0.0812047 - 0.14709426
Average (Standard dev.)-0.0011557305 (±0.017560013)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-80-80-80
Dimensions160160160
Spacing160160160
CellA=B=C: 768.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.84.84.8
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z768.000768.000768.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-38-19-20
NX/NY/NZ858082
MAP C/R/S123
start NC/NR/NS-80-80-80
NC/NR/NS160160160
D min/max/mean-0.0810.147-0.001

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Supplemental data

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Sample components

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Entire : VLDL in complex with antibody mAB012

EntireName: VLDL in complex with antibody mAB012Very low-density lipoprotein
Components
  • Complex: VLDL in complex with antibody mAB012Very low-density lipoprotein
    • Complex: human plasma VLDL
    • Complex: Monoclonal IgG antibody mAB012

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Supramolecule #1: VLDL in complex with antibody mAB012

SupramoleculeName: VLDL in complex with antibody mAB012 / type: complex / ID: 1 / Parent: 0
Details: VLDL was isolated from human plasma by density gradient centrifugation. mAB012 was purchased from EMD Millipore. The monoclonal IgG antibody was designed to recognize the first 10 amino acid ...Details: VLDL was isolated from human plasma by density gradient centrifugation. mAB012 was purchased from EMD Millipore. The monoclonal IgG antibody was designed to recognize the first 10 amino acid residues of apoB-100. IgG fraction was purified from mouse ascites by DEAE column chromatography. Equimolar VLDL and mAB012 were mixed and kept at 4 degC overnight to prepare the complexes.
Source (natural)Organism: Homo sapiens (human) / Tissue: blood
Molecular weightExperimental: 12.0 MDa

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Supramolecule #2: human plasma VLDL

SupramoleculeName: human plasma VLDL / type: complex / ID: 2 / Parent: 1
Details: VLDL was isolated from human plasma by density gradient centrifugation.
Source (natural)Organism: Homo sapiens (human) / Tissue: blood
Molecular weightExperimental: 12.0 MDa

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Supramolecule #3: Monoclonal IgG antibody mAB012

SupramoleculeName: Monoclonal IgG antibody mAB012 / type: complex / ID: 3 / Parent: 1
Details: mAB012 was purchased from EMD Millipore. The monoclonal IgG antibody was designed to recognize the first 10 amino acid residues of apoB-100. IgG fraction was purified from mouse ascites by ...Details: mAB012 was purchased from EMD Millipore. The monoclonal IgG antibody was designed to recognize the first 10 amino acid residues of apoB-100. IgG fraction was purified from mouse ascites by DEAE column chromatography.
Source (natural)Organism: Mus musculus (house mouse) / Tissue: ascites
Molecular weightTheoretical: 160 KDa

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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 chloridesodium 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
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 FIELDBright-field microscopy / Cs: 2.2 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000
Specialist opticsEnergy filter - Name: Zeiss in-column Omega / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
TemperatureMin: 90.0 K / Max: 93.0 K
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Dimensions - Width: 2048 pixel / Digitization - Dimensions - Height: 2048 pixel / Digitization - Sampling interval: 30.0 µm / Number grids imaged: 1 / Number real images: 85 / Average exposure time: 0.5 sec. / Average electron dose: 1.0 e/Å2
Details: Images were collected by using the Gatan Tomography module of Digital Micrograph. XY tracking and focusing were done manually.

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Image processing

CTF correctionSoftware - Name: TOMOCTF (ver. V. October 2012)
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 80.0 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
DetailsDefects in images such as bad pixels and X-rays were removed prior to alignment and 3D reconstruction.

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