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- EMDB-2180: 3D reconstruction of LDL at 37C (human body temperature) using cr... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-2180 | |||||||||
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Title | 3D reconstruction of LDL at 37C (human body temperature) using cryo-EM techniques | |||||||||
![]() | Reconstruction of native LDL at 37C using cryo-EM based single particle reconstruction | |||||||||
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![]() | LDL / native LDL / human body temperature | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 16.0 Å | |||||||||
![]() | Kumar V / Butcher SJ / Oorni K / Engelhardt P / Heikkonen J / Kaski K / Ala-Korpela M / Kovanen PT | |||||||||
![]() | ![]() Title: Three-dimensional cryoEM reconstruction of native LDL particles to 16Å resolution at physiological body temperature. Authors: Vibhor Kumar / Sarah J Butcher / Katariina Öörni / Peter Engelhardt / Jukka Heikkonen / Kimmo Kaski / Mika Ala-Korpela / Petri T Kovanen / ![]() Abstract: BACKGROUND: Low-density lipoprotein (LDL) particles, the major carriers of cholesterol in the human circulation, have a key role in cholesterol physiology and in the development of atherosclerosis. ...BACKGROUND: Low-density lipoprotein (LDL) particles, the major carriers of cholesterol in the human circulation, have a key role in cholesterol physiology and in the development of atherosclerosis. The most prominent structural components in LDL are the core-forming cholesteryl esters (CE) and the particle-encircling single copy of a huge, non-exchangeable protein, the apolipoprotein B-100 (apoB-100). The shape of native LDL particles and the conformation of native apoB-100 on the particles remain incompletely characterized at the physiological human body temperature (37 °C). METHODOLOGY/PRINCIPAL FINDINGS: To study native LDL particles, we applied cryo-electron microscopy to calculate 3D reconstructions of LDL particles in their hydrated state. Images of the particles ...METHODOLOGY/PRINCIPAL FINDINGS: To study native LDL particles, we applied cryo-electron microscopy to calculate 3D reconstructions of LDL particles in their hydrated state. Images of the particles vitrified at 6 °C and 37 °C resulted in reconstructions at ~16 Å resolution at both temperatures. 3D variance map analysis revealed rigid and flexible domains of lipids and apoB-100 at both temperatures. The reconstructions showed less variability at 6 °C than at 37 °C, which reflected increased order of the core CE molecules, rather than decreased mobility of the apoB-100. Compact molecular packing of the core and order in a lipid-binding domain of apoB-100 were observed at 6 °C, but not at 37 °C. At 37 °C we were able to highlight features in the LDL particles that are not clearly separable in 3D maps at 6 °C. Segmentation of apoB-100 density, fitting of lipovitellin X-ray structure, and antibody mapping, jointly revealed the approximate locations of the individual domains of apoB-100 on the surface of native LDL particles. CONCLUSIONS/SIGNIFICANCE: Our study provides molecular background for further understanding of the link between structure and function of native LDL particles at physiological body temperature. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 30.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 8.8 KB 8.8 KB | Display Display | ![]() |
Images | ![]() | 914.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 217.4 KB | Display | ![]() |
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Full document | ![]() | 216.5 KB | Display | |
Data in XML | ![]() | 6.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Reconstruction of native LDL at 37C using cryo-EM based single particle reconstruction | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.4 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 : LDL at 37C
Entire | Name: LDL at 37C |
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Components |
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-Supramolecule #1000: LDL at 37C
Supramolecule | Name: LDL at 37C / type: sample / ID: 1000 Details: Samples were vitrified on Quantifoil holey carbon grids (Quantifoil Micro Tools, GmbH) either at 6C or 37C, allowing pre-equilibration of the sample at the desired temperature for at least ...Details: Samples were vitrified on Quantifoil holey carbon grids (Quantifoil Micro Tools, GmbH) either at 6C or 37C, allowing pre-equilibration of the sample at the desired temperature for at least 45 minutes prior to plunging. Number unique components: 1 |
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-Macromolecule #1: apoB-100
Macromolecule | Name: apoB-100 / type: protein_or_peptide / ID: 1 / Name.synonym: apoB / Recombinant expression: No |
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Source (natural) | Organism: ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE / Instrument: OTHER |
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Electron microscopy
Microscope | FEI TECNAI F20 |
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Date | Dec 30, 2005 |
Image recording | Digitization - Scanner: ZEISS SCAI / Number real images: 26083 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: OTHER |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Image processing
Details | Initially only phase-flipping was carried out to correct for the contrast transfer function. To reduce the effect of image noise and artefacts, an initial single particle reconstruction was made on images de-noised with an information theory [Minimum Description Length (MDL)] based method which we have introduced earlier. Fifty initial class averages were obtained using a reference-free classification of 3000 images by multivariate statistical analysis using parameters, as suggested in EMAN . Angles were assigned using the cross common lines method prior to reconstruction using weighted-back projection. The initial 3D models were low-pass filtered. The 2D image dataset was increased to include all of the particles and iterative refinement continued. After each iteration of the single-particle-reconstruction process only 75% of the images with the highest correlation values were chosen. In order to avoid any bias in 3D reconstruction due to the de-noising, the final reconstructions were made using raw images after being assigned to classes using their de-noised equivalents |
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CTF correction | Details: Each particle |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 29844 |