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- EMDB-9086: Single-Molecule 3D Image of Human Plasma Intermediate-Density Lip... -

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Entry
Database: EMDB / ID: EMD-9086
TitleSingle-Molecule 3D Image of Human Plasma Intermediate-Density Lipoprotein in Complex with Monoclonal Antibody MAB012 (No. 02)
Map dataSingle-Molecule 3D Image of Human Plasma Intermediate-Density Lipoprotein in Complex with Monoclonal Antibody MAB012 (No. 02)
Sample
  • Complex: Human plasma intermediate-density lipoprotein in complex with monoclonal antibody mAB012
    • Complex: Human plasma intermediate-density lipoprotein
    • Complex: Monoclonal IgG antibody mAB012
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodelectron tomography / cryo EM / Resolution: 61.5 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.
History
DepositionSep 3, 2018-
Header (metadata) releaseOct 10, 2018-
Map releaseJan 2, 2019-
UpdateDec 25, 2019-
Current statusDec 25, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9086.png

Downloads & links

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Map

FileDownload / File: emd_9086.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSingle-Molecule 3D Image of Human Plasma Intermediate-Density Lipoprotein in Complex with Monoclonal Antibody MAB012 (No. 02)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.7 Å/pix.
x 192 pix.
= 710.4 Å		3.7 Å/pix.
x 192 pix.
= 710.4 Å		3.7 Å/pix.
x 192 pix.
= 710.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelMovie #1: 0.3
Minimum - Maximum-0.48587534 - 1.1324345
Average (Standard dev.)0.006385419 (±0.07954157)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-96-96-96
Dimensions192192192
Spacing192192192
CellA=B=C: 710.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.73.73.7
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z710.400710.400710.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS-96-96-96
NC/NR/NS192192192
D min/max/mean-0.4861.1320.006

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Supplemental data

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Sample components

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Entire : Human plasma intermediate-density lipoprotein in complex with mon...

EntireName: Human plasma intermediate-density lipoprotein in complex with monoclonal antibody mAB012
Components
  • Complex: Human plasma intermediate-density lipoprotein in complex with monoclonal antibody mAB012
    • Complex: Human plasma intermediate-density lipoprotein
    • Complex: Monoclonal IgG antibody mAB012

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Supramolecule #1: Human plasma intermediate-density lipoprotein in complex with mon...

SupramoleculeName: Human plasma intermediate-density lipoprotein in complex with monoclonal antibody mAB012
type: complex / ID: 1 / Parent: 0
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 ...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.

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Supramolecule #2: Human plasma intermediate-density lipoprotein

SupramoleculeName: Human plasma intermediate-density lipoprotein / type: complex / ID: 2 / Parent: 1
Details: Human intermediate-density lipoproteins (IDLs) were isolated from the plasma of a healthy individual by density gradient ultracentrifugation.
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Monoclonal IgG antibody mAB012

SupramoleculeName: Monoclonal IgG antibody mAB012 / type: complex / ID: 3 / Parent: 1
Details: Mouse monoclonal antibody mAB012, whose epitope located within the first 20 N-terminal residues of human apoB-100, was purchased from EMD Millipore.
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Mus musculus (house mouse)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7 / Details: Dulbecco's phosphate buffered saline (DPBS)
GridModel: Homemade / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Instrument: LEICA EM GP
DetailsHuman 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.
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.11 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 19000
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsX-ray speckles in images were removed before CTF correction.
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 61.5 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.
Number images used: 73
FSC plot (resolution estimation)

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