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- EMDB-9270: Single-Molecule 3D Image of Cholesteryl Ester Transfer Protein by... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9270 | |||||||||
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Title | Single-Molecule 3D Image of Cholesteryl Ester Transfer Protein by Individual-Particle Electron Tomography (No. 01) | |||||||||
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Biological species | ![]() | |||||||||
Method | electron tomography / cryo EM / Resolution: 95.5 Å | |||||||||
![]() | Wu H / Zhai X / Lei D / Liu J / Yu Y / Bie R / Ren G | |||||||||
![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 789.7 KB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.9 KB 9.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.1 KB | Display | ![]() |
Images | ![]() | 10.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9262C ![]() 9263C ![]() 9266C ![]() 9267C ![]() 9268C ![]() 9269C ![]() 9271C C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 4.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Cholesteryl ester transfer protein
Entire | Name: Cholesteryl ester transfer protein |
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Components |
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-Supramolecule #1: Cholesteryl ester transfer protein
Supramolecule | Name: Cholesteryl ester transfer protein / type: organelle_or_cellular_component / ID: 1 / Parent: 0 Details: Cholesteryl ester transfer protein (CETP) was produced by MERCK. |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 2.5 MDa |
Recombinant expression | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | electron tomography |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7 / Details: 1X Dulbeccos phosphate-buffered saline |
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Grid | Model: Homemade / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Instrument: LEICA EM GP |
Details | Cholesteryl ester transfer protein (CETP) was produced by MERCK. |
Sectioning | Other: NO SECTIONING |
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Electron microscopy
Microscope | ZEISS LIBRA120PLUS |
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Specialist optics | Energy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 0.32 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal magnification: 50000 |