|Entry||Database: EMDB / ID: 9070|
|Title||Single-Molecule 3D Image of Human Plasma Intermediate-Density Lipoprotein (No. 02)|
|Map data||primary map|
|Sample||Human plasma intermediate-density lipoprotein:|
|Source||Homo sapiens (human)|
|Method||electron tomography / cryo EM / 96.1 Å resolution|
|Authors||Lei D / Yu Y / Kuang Y / Krauss R / Ren G|
|Citation||Journal: Biochim Biophys Acta Mol Cell Biol Lipids / Year: 2019|
Title: Single-molecule 3D imaging of human plasma intermediate-density lipoproteins reveals a polyhedral structure.
Authors: Dongsheng Lei / Yadong Yu / Yu-Lin Kuang / Jianfang Liu / Ronald M Krauss / Gang Ren
Abstract: Intermediate-density lipoproteins (IDLs), the remnants of very-low-density lipoproteins via lipolysis, are rich in cholesteryl ester and are associated with cardiovascular disease. Despite ...Intermediate-density lipoproteins (IDLs), the remnants of very-low-density lipoproteins via lipolysis, are rich in cholesteryl ester and are associated with cardiovascular disease. Despite pharmacological interest in IDLs, their three-dimensional (3D) structure is still undetermined due to their variation in size, composition, and dynamic structure. To explore the 3D structure of IDLs, we reconstructed 3D density maps from individual IDL particles using cryo-electron microscopy (cryo-EM) and individual-particle electron tomography (IPET, without averaging from different molecules). 3D reconstructions of IDLs revealed an unexpected polyhedral structure that deviates from the generally assumed spherical shape model (Frias et al., 2007; Olson, 1998; Shen et al., 1977). The polyhedral-shaped IDL contains a high-density shell formed by flat surfaces that are similar to those of very-low-density lipoproteins but have sharper dihedral angles between nearby surfaces. These flat surfaces would be less hydrophobic than the curved surface of mature spherical high-density lipoprotein (HDL), leading to a lower binding affinity of IDL to hydrophobic proteins (such as cholesteryl ester transfer protein) than HDL. This is the first visualization of the IDL 3D structure, which could provide fundamental clues for delineating the role of IDL in lipid metabolism and cardiovascular disease.
|Date||Deposition: Sep 3, 2018 / Header (metadata) release: Oct 31, 2018 / Map release: Jan 16, 2019 / Last update: Jan 16, 2019|
|Structure viewer||EM map: |
Downloads & links
|File||emd_9070.map.gz (map file in CCP4 format, 28312 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 2.4 Å|
CCP4 map header:
-Entire Human plasma intermediate-density lipoprotein
|Entire||Name: Human plasma intermediate-density lipoprotein / Number of components: 1|
-Component #1: cellular-component, Human plasma intermediate-density lipoprotein
|Cellular-component||Name: Human plasma intermediate-density lipoprotein / Recombinant expression: No|
|Mass||Experimental: 3 MDa|
|Source||Species: Homo sapiens (human)|
|Source (natural)||Organ or tissue: Blood|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||Specimen conc.: 2 mg/ml|
Buffer solution: Dulbecco's phosphate buffered saline (DPBS)
|Vitrification||Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 80 %|
-Electron microscopy imaging
|Imaging||Microscope: ZEISS LIBRA120PLUS|
|Electron gun||Electron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 1.45 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 50000.0 X (nominal) / Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Energy filter: In-column Omega Filter|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN ULTRASCAN 4000 (4k x 4k)|
-Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi