|Entry||Database: EMDB / ID: EMD-4651|
|Title||Packaging of DNA Origami in Viral Capsids|
|Sample||Simian virus 40:|
|Source||Simian virus 40|
|Method||single particle reconstruction / cryo EM / Resolution: 21 Å|
|Authors||Kopatz I / Zalk R / Levi-Kalisman Y / Zlotkin-Rivkin E / Frank GA / Kler S|
|Citation||Journal: Nanoscale / Year: 2019|
Title: Packaging of DNA origami in viral capsids.
Authors: Idit Kopatz / Ran Zalk / Yael Levi-Kalisman / Efrat Zlotkin-Rivkin / Gabriel A Frank / Stanislav Kler /
Abstract: Here we show the encapsulation of 35 nm diameter, nearly-spherical, DNA origami by self-assembly of SV40-like (simian virus 40) particles. The self-assembly of this new type of nanoparticles is ...Here we show the encapsulation of 35 nm diameter, nearly-spherical, DNA origami by self-assembly of SV40-like (simian virus 40) particles. The self-assembly of this new type of nanoparticles is highly reproducible and efficient. The structure of these particles was determined by cryo-EM. The capsid forms a regular SV40 lattice of T = 7d icosahedral symmetry and the structural features of encapsulated DNA origami are fully visible. These particles are a promising biomaterial for use in various medical applications.
|Date||Deposition: Mar 1, 2019 / Header (metadata) release: May 1, 2019 / Map release: May 1, 2019 / Update: May 1, 2019|
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_4651.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 2.3 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Simian virus 40
|Entire||Name: Simian virus 40 / Number of components: 1|
-Component #1: virus, Simian virus 40
|Virus||Name: Simian virus 40SV40 / Class: VIRUS-LIKE PARTICLE / Empty: No / Enveloped: No / Isolate: OTHER|
|Species||Species: Simian virus 40|
|Source (engineered)||Expression System: Spodoptera frugiperda (fall armyworm)|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||pH: 7.2|
|Vitrification||Instrument: LEICA EM GP / Cryogen name: ETHANE / Temperature: 293 K / Humidity: 96 %|
-Electron microscopy imaging
Model: Tecnai Polara / Image courtesy: FEI Company
|Imaging||Microscope: FEI POLARA 300|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 100 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD / Energy filter: GIF Quantum LS|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Processing||Method: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 7939|
|3D reconstruction||Software: RELION / Resolution: 21 Å / Resolution method: FSC 0.143 CUT-OFF|
-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