|Entry||Database: EMDB / ID: 5006|
|Title||Structure of immature Dengue virus at low pH|
|Keywords||Dengue virus / maturation|
|Sample||immature Dengue virus|
|Source||Dengue virus / virus / Dengue / デングウイルス|
|Map data||immature Dengue virus particle at pH 6|
|Method||single particle (icosahedral) reconstruction, at 25 Å resolution|
|Authors||Yu I / Zhang W / Holdaway HA / Li L / Kostyuchenko VA / Chipman PR / Kuhn RJ / Rossmann MG / Chen J|
|Citation||Science, 2008, 319, 1834-1837|
|Validation Report||PDB-ID: 3c6r|
SummaryFull reportAbout validation report
|Date||Deposition: Feb 26, 2008 / Header (metadata) release: Mar 4, 2008 / Map release: Apr 22, 2009 / Last update: Jul 8, 2011|
Downloads & links
|File||emd_5006.map.gz (map file in CCP4 format, 64772 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 2.74 Å|
CCP4 map header:
-Entire immature Dengue virus
|Entire||Name: immature Dengue virus / Number of components: 1|
-Component #1: virus, Dengue virus
|Virus||Name: Dengue virus / a.k.a: Dengue / Class: VIRION / Empty: No / Enveloped: Yes / Isolate: STRAIN|
|Species||Species: Dengue virus / virus / Dengue / デングウイルス|
|Source (natural)||Host category: VERTEBRATES|
|Sample solution||Buffer solution: The virus was mixed in NTE buffer (10 mM Tris, 120 mM NaCl, and 1 mM EDTA at pH 8) with 50 mM MES, 120 mM NaCl at pH 5.6 to yield a final pH of 6|
|Support film||400 mesh copper grid|
|Vitrification||Instrument: NONE / 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 predetermined 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.
-Electron microscopy imaging
|Imaging||Microscope: FEI/PHILIPS CM200FEG|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 17 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 50000 X (nominal), 51040 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1400 - 2900 nm|
|Specimen Holder||Holder: Eucentric / Model: GATAN LIQUID NITROGEN / Temperature: 98 K|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 14 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 12 / OD range: 1|
|Processing||Method: single particle (icosahedral) reconstruction / Number of projections: 231 / Applied symmetry: I (icosahedral)|
|3D reconstruction||Algorithm: Fourier-Bessel Method / Euler angles: theta:69-90 degrees phi:(-31)-31 degrees / Software: EM3DR / CTF correction: each particle / Resolution: 25 Å / Resolution method: FSC 0.5|
-Atomic model buiding
-Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
- Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
- Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
- Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.
External links: The 2017 Nobel Prize in Chemistry - Press Release
-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)
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