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- EMDB-9271: Single-Molecule 3D Image of Cholesteryl Ester Transfer Protein by... -

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Basic information

Entry
Database: EMDB / ID: 9271
TitleSingle-Molecule 3D Image of Cholesteryl Ester Transfer Protein by Individual-Particle Electron Tomography (No. 02)
Map data
SampleCholesteryl ester transfer protein:
SourceHomo sapiens (human)
Methodelectron tomography / cryo EM / 95.5 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: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9271.map.gz (map file in CCP4 format, 865 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
60 pix
4.8 Å/pix.
= 288. Å
60 pix
4.8 Å/pix.
= 288. Å
60 pix
4.8 Å/pix.
= 288. Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.8 Å
Density
Contour Level:1 (movie #1):
Minimum - Maximum-0.39537612 - 2.5413465
Average (Standard dev.)0.048508577 (0.21289736)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions606060
Origin-30.0-30.0-30.0
Limit29.029.029.0
Spacing606060
CellA=B=C: 288.0 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/z606060
origin x/y/z0.0000.0000.000
length x/y/z288.000288.000288.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-30-30-30
NC/NR/NS606060
D min/max/mean-0.3952.5410.049

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Supplemental data

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Sample components

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Entire Cholesteryl ester transfer protein

EntireName: Cholesteryl ester transfer protein
Details: Cholesteryl ester transfer protein (CETP) was produced by MERCK.
Number of components: 1

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Component #1: 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
MassTheoretical: 2.5 MDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Cricetulus griseus (Chinese hamster) / Strain: DG44 / Cell of expression system: Ovary
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: 0.32 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: 95.5 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 7 nm.
FSC plot
(resolution estimation)

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