|Entry||Database: EMDB / ID: 1307|
|Title||Electron cryotomography reveals the portal in the herpesvirus capsid.|
|Sample||Herpes Simplex Virus 1|
|Source||Human herpesvirus 1 / virus / Herpes Simplex / ヒトヘルペスウイルス 1|
|Map data||This is the 5-fold-averaged map.|
|Authors||Chang JT / Schmid MF / Rixon FJ / Chiu W|
|Citation||J. Virol., 2007, 81, 2065-2068|
|Date||Deposition: Nov 25, 2006 / Header (metadata) release: Dec 6, 2006 / Map release: Dec 6, 2007 / Last update: Oct 24, 2012|
Downloads & links
|File||emd_1307.map.gz (map file in CCP4 format, 93313 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 5.43 Å|
CCP4 map header:
-Entire Herpes Simplex Virus 1
|Entire||Name: Herpes Simplex Virus 1 / Number of components: 1|
-Component #1: virus, Human herpesvirus 1
|Virus||Name: Human herpesvirus 1 / a.k.a: Herpes Simplex / Class: VIRION / Empty: Yes / Enveloped: No / Isolate: SPECIES|
|Species||Species: Human herpesvirus 1 / virus / Herpes Simplex / ヒトヘルペスウイルス 1|
|Source (natural)||Host Species: Homo sapiens / human / Host category: INVERTEBRATES|
|Shell #1||Name of element: Capsid / Diameter: 1250 Å / T number(triangulation number): 16|
|Sample solution||Buffer solution: 170mM NaCl, 3.4mM KCl, 10mM Na2HPO4, 1.8mM KH2PO4, 6.8mM CaCl2, 4.9mM MgCl2|
|Support film||200 mesh copper grid|
|Vitrification||Instrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 293 K / Humidity: 100 % / Details: Vitrification instrument: Vitrobot|
-Electron microscopy imaging
|Imaging||Microscope: JEOL 2010F|
Details: Tilted from -70 to +70 in 2 degree increments using Mr T software (unpublished).
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 20000 X (nominal), 27680 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 3000 nm|
|Specimen Holder||Holder: Side entry liquid nitrogen cooled / Model: GATAN LIQUID NITROGEN / Tilt Angle: 70 - 70 deg. / Temperature: 93 K ( 93 - 93 K)|
|Camera||Detector: GENERIC GATAN|
|Processing||Method: subtomogram averaging|
Details: Averaged 13 particles extracted from the reconstruction. Average number of tilts used in the 3D reconstructions: 71. Average tomographic tilt angle increment: 2.
|3D reconstruction||Algorithm: Weighted backprojection / Software: IMOD / Details: 5-fold-averaged|
-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