|Entry||Database: EMDB / ID: 5380|
|Title||Cryo-EM 3D reconstruction of empty Triatoma Virus (corresponding to a suspension of full TrV heated)|
|Map data||3D reconstruction of empty TrV|
|Sample||Empty TrV particles:|
|Keywords||Triatoma virus / Dicistrovirus / cryo-electron microscopy / 3D reconstruction / RNA delivery|
|Source||Triatoma virus (TrV)|
|Method||single particle reconstruction / cryo EM / 22 Å resolution|
|Authors||Neumann E / Agirre J / Goret G / Legoff M / Marti GA / Navaza J / Guerin DMA|
|Citation||Journal: J. Gen. Virol. / Year: 2013|
Title: Cryo-electron microscopy reconstructions of triatoma virus particles: a clue to unravel genome delivery and capsid disassembly.
Authors: J Agirre / G Goret / M LeGoff / R Sánchez-Eugenia / G A Marti / J Navaza / D M A Guérin / E Neumann
|Date||Deposition: Jan 6, 2012 / Header (metadata) release: Jan 13, 2012 / Map release: Feb 13, 2013 / Last update: Aug 14, 2013|
|Structure viewer||EM map: |
Downloads & links
|File||emd_5380.map.gz (map file in CCP4 format, 64772 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.77 Å|
CCP4 map header:
-Entire Empty TrV particles
|Entire||Name: Empty TrV particles / Number of components: 1|
-Component #1: virus, Triatoma virus
|Virus||Name: Triatoma virus / a.k.a: TrV / Class: VIRION / Empty: Yes / Enveloped: No / Isolate: OTHER|
|Species||Species: Triatoma virus (TrV)|
|Source (natural)||Host category: INVERTEBRATES|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||Buffer solution: NMT (10 mM NaCl, 1 mM MgCl2, 50 mM Tris-HCl)|
|Support film||400 mesh quantifoil grid|
|Vitrification||Instrument: FEI VITROBOT / Cryogen name: ETHANE / Details: Vitrification instrument: Vitrobot FEI|
-Electron microscopy imaging
|Imaging||Microscope: FEI/PHILIPS CM200T|
|Electron gun||Electron source: LAB6 / Accelerating voltage: 200 kV / Illumination mode: OTHER|
|Lens||Magnification: 38000 X (nominal), 39500 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200 - 4000 nm|
|Specimen Holder||Holder: Side entry liquid nitrogen-cooled cryo specimen holder|
Model: GATAN LIQUID NITROGEN
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 15 / Scanner: ZEISS SCAI / Sampling size: 7 microns|
|Processing||Method: single particle reconstruction / Number of projections: 573 / Applied symmetry: I (icosahedral)|
|3D reconstruction||Software: EM3DR2 / Resolution: 22 Å / Resolution method: FSC 0.5|
-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