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- EMDB-9094: Single-Molecule 3D Image of Two Human Plasma Intermediate-Density... -

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Basic information

Entry
Database: EMDB / ID: 9094
TitleSingle-Molecule 3D Image of Two Human Plasma Intermediate-Density Lipoproteins in Complex with One Monoclonal Antibody MAB012 (No. 03)
Map dataTwo Human Plasma Intermediate-Density Lipoproteins in Complex with One Monoclonal Antibody MAB012 (No. 03)
SampleTwo human plasma intermediate-density lipoproteins in complex with one monoclonal antibody mAB012
  • Human plasma intermediate-density lipoprotein
  • Monoclonal IgG antibody mAB012
SourceHomo sapiens (human) / Mus musculus (house mouse)
Methodelectron tomography / cryo EM / 68.6 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: Sep 26, 2018 / Map release: Jan 9, 2019 / Last update: Jan 9, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9094.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
3.7 Å/pix.
= 947.2 Å
256 pix
3.7 Å/pix.
= 947.2 Å
256 pix
3.7 Å/pix.
= 947.2 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.7 Å
Density
Contour Level:0.2 (movie #1):
Minimum - Maximum-0.33893687 - 0.9899391
Average (Standard dev.)0.0050917715 (0.061832182)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin-128.0-128.0-128.0
Limit127.0127.0127.0
Spacing256256256
CellA=B=C: 947.2 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.73.73.7
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z947.200947.200947.200
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-0.3390.9900.005

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Supplemental data

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Sample components

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Entire Two human plasma intermediate-density lipoproteins in complex wit...

EntireName: Two human plasma intermediate-density lipoproteins in complex with one monoclonal antibody mAB012
Details: Human intermediate-density lipoproteins (IDLs) were isolated from the plasma of a healthy individual by density gradient ultracentrifugation. Mouse monoclonal antibody mAB012, whose epitope located within the first 20 N-terminal residues of human apoB-100, was purchased from EMD Millipore. The antigen-antibody complex was prepared by incubating IDLs and mAB012 in a molar ratio of 1:2.3 at 4 degC overnight.
Number of components: 3

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Component #1: protein, Two human plasma intermediate-density lipoproteins in co...

ProteinName: Two human plasma intermediate-density lipoproteins in complex with one monoclonal antibody mAB012
Details: Human intermediate-density lipoproteins (IDLs) were isolated from the plasma of a healthy individual by density gradient ultracentrifugation. Mouse monoclonal antibody mAB012, whose epitope located within the first 20 N-terminal residues of human apoB-100, was purchased from EMD Millipore. The antigen-antibody complex was prepared by incubating IDLs and mAB012 in a molar ratio of 1:2.3 at 4 degC overnight.
Recombinant expression: No

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Component #2: protein, Human plasma intermediate-density lipoprotein

ProteinName: Human plasma intermediate-density lipoprotein
Details: Human intermediate-density lipoproteins (IDLs) were isolated from the plasma of a healthy individual by density gradient ultracentrifugation.
Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Component #3: protein, Monoclonal IgG antibody mAB012

ProteinName: Monoclonal IgG antibody mAB012
Details: Mouse monoclonal antibody mAB012, whose epitope located within the first 20 N-terminal residues of human apoB-100, was purchased from EMD Millipore.
Recombinant expression: No
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Mus musculus (house mouse)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionBuffer 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

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 1.11 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 19000.0 X (nominal) / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: electron tomography / Number of sections: 58
Details: X-ray speckles in images were removed before CTF correction.
3D reconstructionAlgorithm: FOURIER SPACE / Resolution: 68.6 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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