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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: 9269
TitleSingle-Molecule 3D Image of Low-Density Lipoprotein in Complex with Cholesteryl Ester Transfer Protein (No. 02)
Map data
SampleHuman plasma low-density lipoprotein in complex with cholesteryl ester transfer protein:
Human plasma low-density lipoprotein / Cholesteryl ester transfer protein
SourceHomo sapiens (human)
Methodelectron tomography / cryo EM / 71 Å resolution
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
DateDeposition: Oct 27, 2018 / Header (metadata) release: Nov 28, 2018 / Map release: Nov 28, 2018 / Last update: Nov 28, 2018

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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

Fileemd_9269.map.gz (map file in CCP4 format, 4001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
100 pix
4.8 Å/pix.
= 480. Å		100 pix
4.8 Å/pix.
= 480. Å		100 pix
4.8 Å/pix.
= 480. Å

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 Level:0.3 (movie #1):
Minimum - Maximum-0.3867251 - 1.2899266
Average (Standard dev.)0.03146992 (0.15179084)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions100100100
Origin-50.0-50.0-50.0
Limit49.049.049.0
Spacing100100100
CellA=B=C: 480.00003 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
NX/NY/NZ
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
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.
Number of components: 3

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Component #1: protein, Human plasma low-density lipoprotein in complex with cho...

ProteinName: Human plasma low-density lipoprotein in complex with 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.
Recombinant expression: No
MassTheoretical: 2.5 MDa
SourceSpecies: Homo sapiens (human)

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

ProteinName: Human plasma low-density lipoprotein
Details: Low-density lipoproteins (LDLs) were isolated from human plasma by density gradient ultracentrifugation (Children's Hospital Oakland Research Institute).
Recombinant expression: No

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Component #3: cellular-component, Cholesteryl ester transfer protein

Cellular-componentName: Cholesteryl ester transfer protein
Details: Cholesteryl ester transfer protein (CETP) was produced by MERCK.
Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (natural)Organ or tissue: Blood

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionBuffer solution: 1X Dulbeccos phosphate-buffered saline / pH: 7
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 %

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Electron microscopy imaging

ImagingMicroscope: ZEISS LIBRA120PLUS
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 0.26 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000.0 X (nominal) / Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Energy filter: In-column Omega Filter
Specimen HolderModel: OTHER
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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Image processing

ProcessingMethod: electron tomography / Number of sections: 77
Details: X-ray speckles in images were removed before CTF correction.
3D reconstructionAlgorithm: FOURIER SPACE / Resolution: 71 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.
FSC plot
(resolution estimation)

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