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- EMDB-9269: Single-Molecule 3D Image of Low-Density Lipoprotein in Complex wi... -

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Basic information

Entry
Database: EMDB / ID: EMD-9269
TitleSingle-Molecule 3D Image of Low-Density Lipoprotein in Complex with Cholesteryl Ester Transfer Protein (No. 02)
Map data
Sample
  • Complex: Human plasma low-density lipoprotein in complex with cholesteryl ester transfer protein
    • Complex: Human plasma low-density lipoprotein
    • Organelle or cellular component: Cholesteryl ester transfer protein
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM / Resolution: 71.0 Å
AuthorsWu H / Zhai X / Lei D / Liu J / Yu Y / Bie R / Ren G
CitationJournal: Sci Rep / Year: 2018
Title: An Algorithm for Enhancing the Image Contrast of Electron Tomography.
Authors: Hao Wu / Xiaobo Zhai / Dongsheng Lei / Jianfang Liu / Yadong Yu / Rongfang Bie / Gang Ren /
Abstract: Three-dimensional (3D) reconstruction of a single protein molecule is essential for understanding the relationship between the structural dynamics and functions of the protein. Electron tomography ...Three-dimensional (3D) reconstruction of a single protein molecule is essential for understanding the relationship between the structural dynamics and functions of the protein. Electron tomography (ET) provides a tool for imaging an individual particle of protein from a series of tilted angles. Individual-particle electron tomography (IPET) provides an approach for reconstructing a 3D density map from a single targeted protein particle (without averaging from different particles of this type of protein), in which the target particle was imaged from a series of tilting angles. However, owing to radiation damage limitations, low-dose images (high noise, and low image contrast) are often challenging to be aligned for 3D reconstruction at intermediate resolution (1-3 nm). Here, we propose a computational method to enhance the image contrast, without increasing any experimental dose, for IPET 3D reconstruction. Using an edge-preserving smoothing-based multi-scale image decomposition algorithm, this method can detect the object against a high-noise background and enhance the object image contrast without increasing the noise level or significantly decreasing the image resolution. The method was validated by using both negative staining (NS) ET and cryo-ET images. The successful 3D reconstruction of a small molecule (<100 kDa) indicated that this method can be used as a supporting tool to current ET 3D reconstruction methods for studying protein dynamics via structure determination from each individual particle of the same type of protein.
History
DepositionOct 27, 2018-
Header (metadata) releaseNov 28, 2018-
Map releaseNov 28, 2018-
UpdateNov 28, 2018-
Current statusNov 28, 2018Processing 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
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9269.png

Downloads & links

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Map

FileDownload / File: emd_9269.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.8 Å/pix.
x 100 pix.
= 480. Å		4.8 Å/pix.
x 100 pix.
= 480. Å		4.8 Å/pix.
x 100 pix.
= 480. 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: 0.3
Minimum - Maximum-0.3867251 - 1.2899266
Average (Standard dev.)0.03146992 (±0.15179084)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-50
Dimensions100100100
Spacing100100100
CellA=B=C: 480.00003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.84.84.8
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z480.000480.000480.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-50-50-50
NC/NR/NS100100100
D min/max/mean-0.3871.2900.031

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Supplemental data

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Sample components

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Entire : Human plasma low-density lipoprotein in complex with cholesteryl ...

EntireName: Human plasma low-density lipoprotein in complex with cholesteryl ester transfer protein
Components
  • Complex: Human plasma low-density lipoprotein in complex with cholesteryl ester transfer protein
    • Complex: Human plasma low-density lipoprotein
    • Organelle or cellular component: Cholesteryl ester transfer protein

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Supramolecule #1: Human plasma low-density lipoprotein in complex with cholesteryl ...

SupramoleculeName: Human plasma low-density lipoprotein in complex with cholesteryl ester transfer protein
type: complex / ID: 1 / Parent: 0
Details: Low-density lipoproteins (LDLs) were isolated from human plasma by density gradient ultracentrifugation (Children's Hospital Oakland Research Institute). Cholesteryl ester transfer protein ...Details: Low-density lipoproteins (LDLs) were isolated from human plasma by density gradient ultracentrifugation (Children's Hospital Oakland Research Institute). Cholesteryl ester transfer protein (CETP) was produced by MERCK. LDL and CETP were incubated at 37 degC for 15 minutes at a molar ratio of ~4:1.
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 2.5 MDa

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Supramolecule #2: Human plasma low-density lipoprotein

SupramoleculeName: Human plasma low-density lipoprotein / type: complex / ID: 2 / Parent: 1
Details: Low-density lipoproteins (LDLs) were isolated from human plasma by density gradient ultracentrifugation (Children's Hospital Oakland Research Institute).

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Supramolecule #3: Cholesteryl ester transfer protein

SupramoleculeName: Cholesteryl ester transfer protein / type: organelle_or_cellular_component / ID: 3 / Parent: 1
Details: Cholesteryl ester transfer protein (CETP) was produced by MERCK.
Source (natural)Organism: Homo sapiens (human) / Tissue: Blood

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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: 1X Dulbeccos phosphate-buffered saline
GridModel: Homemade / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: LEICA EM GP
DetailsLow-density lipoproteins (LDLs) were isolated from human plasma by density gradient ultracentrifugation (Children's Hospital Oakland Research Institute). Cholesteryl ester transfer protein (CETP) was produced by MERCK. LDL and CETP were incubated at 37 degC for 15 minutes at a molar ratio of ~4:1.
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeZEISS LIBRA120PLUS
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 0.26 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal magnification: 50000

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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: 71.0 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 7 nm.
Number images used: 77
CTF correctionSoftware - Name: TOMOCTF
FSC plot (resolution estimation)

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