|Entry||Database: EMDB / ID: 1421|
|Title||Electron cryomicroscopy reveals different F1+F2 protein States in intact parainfluenza virions.|
|Sample||F-Protein in intact Parainfluenzavirus 5|
|Source||Parainfluenza virus 5 / virus|
|Map data||In-situ 3D reconstruction of the ectodomain of the PIV5 F protein determined from cryo-negative stain electron micrographs|
|Method||single particle reconstruction, at 15 Å resolution|
|Authors||Ludwig K / Schade B / Boettcher C / Korte T|
|Citation||J. Virol., 2008, 82, 3775-3781|
|Date||Deposition: Sep 7, 2007 / Header (metadata) release: Sep 11, 2007 / Map release: Apr 7, 2008 / Last update: Oct 24, 2012|
Downloads & links
|File||emd_1421.map.gz (map file in CCP4 format, 1301 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.56 Å|
CCP4 map header:
-Entire F-Protein in intact Parainfluenzavirus 5
|Entire||Name: F-Protein in intact Parainfluenzavirus 5|
Details: sample of fusion active virions (proven by fluorescence spectroscopy)of PIV5 (strain W3A)
Number of components: 1 / Oligomeric State: F-Protein Homotrimer
|Mass||Theoretical: 150 kDa|
-Component #1: protein, F-Protein
|Protein||Name: F-Protein / Oligomeric Details: Homotrimer / Recombinant expression: No|
|Mass||Experimental: 150 kDa|
|Source||Species: Parainfluenza virus 5 / virus / Strain: W3A|
|Source (natural)||Location in cell: viral membrane|
|Sample solution||Buffer solution: PBS (150 mM NaCl, 5.8 mM NaH2PO4/Na2HPO4) / pH: 7.4|
|Support film||200 mesh carbon coated collodium-supported copper grids|
|Staining||30 seconds absorption 60 seconds staining (1% phospho-tungstic acid, pH 7.4) vitrified in liquid ethane|
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE|
Method: A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. Once the ethane in the vial is completely frozen, it needs to be slightly melted. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot of excess buffer, sufficient to leave a thin layer on the grid. After a redetermined time, the filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen,and the grid is transferred under liquid nitrogen to a storage box immersed liquid nitrogen for later use in the microscope.
Details: Vitrification instrument: self-construction
-Electron microscopy imaging
Model: Tecnai F20 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F20|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 160 kV / Electron dose: 12 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 50000 X (nominal), 51064 X (calibrated)|
Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1501 - 2066 nm
|Specimen Holder||Holder: Side entry liquid nitrogen-cooled cryo specimen holder|
Model: GATAN LIQUID NITROGEN / Temperature: 92 K
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 175 / Scanner: PRIMESCAN / Sampling size: 4 microns / Bit depth: 8|
|Processing||Method: single particle reconstruction / Number of projections: 5700|
Details: well resolved spike-like proteins protruding from the viral membrane suitable for single particle analysis were interactively selected
Applied symmetry: C3 (3 fold cyclic)
|3D reconstruction||Algorithm: Common lines / Software: Imagic / CTF correction: MSA-based / Resolution: 15 Å / Resolution method: FSC 3 SIGMA|
-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 / EM Navigator (legacy version) / Yorodumi (legacy version)
+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 / EM Navigator (legacy version) / Yorodumi (legacy version)
+Apr 13, 2016. Omokage search got faster
Omokage search got faster
- The computation time became ~1/2 compared to the previous version by re-optimization of data accession
- Enjoy "shape similarity" of biomolecules, more!
Related info.: Omokage search
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- All the functionalities will be ported from the levgacy version.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi