Results: 5

1.
Figure 1

Figure 1. Cryo-EM images of LDL. From: Enhancing the Contrast of ApoB to Locate the Surface Components in the 3D Density Map of Human LDL.

a. Electron micrograph of LDL in vitreous ice, electron dense object appears as dark region on the micrograph. b. Typical LDL projection views in the electron micrograph. Triangles indicate the individual particles with the “pointed feature”.

Yuhang Liu, et al. J Mol Biol. ;405(1):274-283.
2.
Figure 5

Figure 5. Proposed lipid packing model in LDL. From: Enhancing the Contrast of ApoB to Locate the Surface Components in the 3D Density Map of Human LDL.

Cholesteryl palmitate and dipalmitoyl-phosphatidylcholine (green) were used to build the model. The sterol rings are colored in orange and the acyl chains from cholesteryl palmitate are colored in white. The phosphorus atoms are colored in purple. A slice of the unlabeled LDL structure with the inside alternating density feature is shown in the background at the same scale. The color indicates the intensity values within the slice as Red > Yellow > Grey.

Yuhang Liu, et al. J Mol Biol. ;405(1):274-283.
3.
Figure 4

Figure 4. Comparing EYPC+CO emulsion and LDL particle striped images. From: Enhancing the Contrast of ApoB to Locate the Surface Components in the 3D Density Map of Human LDL.

a. Selected views of the EYPC+CO emulsion in cryo-EM micrograph. Within the rectangular area, the pixel value in each column are summed and plotted with the distance between the columns. The electron dense object appears as dark region. The chemical compositions of the peaks are indicated. b. A class average image with the stripes. Contrast is inverted from the micrograph as electron dense object appears as white region. The pixel value is read along the arrow, the value of the pixels and the distance is plotted on the right. In both plots, the intensity is normalized (see methods section) and the distance between the peaks is indicated above the curve.

Yuhang Liu, et al. J Mol Biol. ;405(1):274-283.
4.
Figure 2

Figure 2. Refinement convergence of LDL and undecagold labeled LDL. From: Enhancing the Contrast of ApoB to Locate the Surface Components in the 3D Density Map of Human LDL.

Comparison of the iso-surface structure volume with the projection map and the class averages. The first, second, and third columns are different views of the same structure rotated 90. The upper three images are the iso-surface display of the reconstructed LDL volume. The middle three images are the projection images corresponding to the same orientation as the iso-surface images; the lower three images are the average image from the class that match the projection view. Contrast is inverted from the micrograph as electron dense object appears as white region in panel Fourier Shell Correlation (FSC) curve calculated from structures reconstructed from odd and even numbered particle images. a. Reconstruction for LDL. The arrows indicate the position of the protrusion. b. Reconstruction for undecagold labeled LDL sample.

Yuhang Liu, et al. J Mol Biol. ;405(1):274-283.
5.
Figure 3

Figure 3. Density distribution at the surface of LDL and undecagold labeled LDL. From: Enhancing the Contrast of ApoB to Locate the Surface Components in the 3D Density Map of Human LDL.

Two volumes were aligned with EMAN program. For the underlying transparent grey structure, the threshold in the voxel density histogram was chosen to display the overall shape (~0.8σ and ~1.4σ for unlabeled and labeled LDL respectively). The overlaid structure was turned 90 in each frame and displayed from left → right in the first row and right → left in the second row. The orientations of the structure are arbitrary defined and indicated as “front”, “back”, “top” and “bottom”. In the “top” and “bottom” views, the arrows indicate the low density regions at the flat surfaces. a. Iso-surface display of LDL structure (transparent gray) overlaid with the higher density regions. The threshold contour level (~4σ) was chosen to include a volume corresponding to the volume of apoB (blue). b. The iso-surface display for undecagold labeled LDL structure volume overlaid with the higher density regions (threshold ~4.6σ) from gold contribution determined as described in Methods (yellow). c. Overlay of the high density regions in the structures of the two volumes shown in a and b. The high density regions from the unlabeled LDL are in transparent blue and the high density regions from undecagold labeled LDL are in yellow mesh.

Yuhang Liu, et al. J Mol Biol. ;405(1):274-283.

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