3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
Electron cryotomography reveals the portal in the herpesvirus capsid.
by subtomogram averaging
#1: Surface view with section colored by density value, Surface level: 0.12, Made by UCSF CHIMERA
#2: Surface view colored by radius, Surface level: 0.12, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 1307 |
|---|---|
| Authors | Chang JT, Schmid MF, Rixon FJ, Chiu W |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 0.12, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 0.12, Made by UCSF CHIMERA |
| Supplemental images | |
| Structure viewers |  Yorodumi,  Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - Primary | |
| Article | J. Virol., Vol. 81, Issue 4, Page 2065-8, Year 2007 |
|---|---|
| Title | Electron cryotomography reveals the portal in the herpesvirus capsid. |
| Authors | Juan T Chang, Michael F Schmid, Frazer J Rixon, Wah Chiu Graduate Program in Structural and Computational Biology and Molecular Biophysics, National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA. |
| Keywords |  Capsid (chemistry), Capsid Proteins (isolation & purification), Cryoelectron Microscopy, Electrophoresis, Polyacrylamide Gel, Herpesvirus 1, Human (chemistry), Models, Molecular, Tomography, Urea (57-13-6) |
| Links | DOI: 10.1128/JVI.02053-06, PubMed: 17151101, PMC: PMC1797573 |
 Map | |||||||||||||||||||||||||
| File |  EMD-1307.map ( map file in CCP4 format, 95552 KB ) | ||||||||||||||||||||||||
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| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
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| Data Type | float (32-bit) | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
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| Unit Cell | A = 1563.84 A , B = 1563.84 A , C = 1563.84 A , alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X = 5.43 A , Y = 5.43 A , Z = 5.43 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | This is the 5-fold-averaged map. | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | Herpes Simplex Virus 1 |
|---|---|
| Number of Components | 1 |
| Component #1: virus - Herpes Simplex | |
| Scientific name | Human herpesvirus 1 |
| Common Name | Herpes Simplex |
| Scientific Name of Species | Human herpesvirus 1 (NCBI Taxonomy: 10298) |
| Common Name of Species | Herpes Simplex |
| Empty | Yes |
| Enveloped | No |
| Isolate | SPECIES |
| Class | VIRION |
| Natural Source | Host Species: Homo sapiens (NCBI Taxonomy: 9606) Host Category: INVERTEBRATES |
| Shell | Diameter: 1250 A Name Element: Capsid T Number: 16 |
 Experiment | |
| Sample Preparation | |
| Specimen Support Details | 200 mesh copper grid |
|---|---|
| Buffer | Details: 170mM NaCl, 3.4mM KCl, 10mM Na2HPO4, 1.8mM KH2PO4, 6.8mM CaCl2, 4.9mM MgCl2 pH: 7.2 |
| Vitrification | |
| Cryogen Name | ETHANE |
| Humidity | 100 |
| Temperature | 293 Kelvin |
| Instrument | FEI VITROBOT |
| Details | Vitrification instrument: Vitrobot |
| 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/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 20000 X, Calibrated: 27680 X |
| Nominal Cs | 2 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 3000 nm - 3000 nm |
| Specimen Holder | |
| Holder | Side entry liquid nitrogen cooled ( GATAN LIQUID NITROGEN ) |
| Tilt Angle | 70 degrees - 70 degrees |
| Temperature | 93 Kelvin ( 93 Kelvin - 93 Kelvin ) |
| Camera | |
| Detector | Gatan |
| Image Acquisition | |
 Processing | |
| Method | subtomogram averaging |
|---|---|
| 3 D reconstruction | |
| Algorithm | Weighted backprojection |
| Software | IMOD |
| Details | 5-fold-averaged |
| 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. |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-1307.xml (7 KB) | ||
|---|---|---|---|
| Map data | emd_1307.map.gz (52.4 MB) | ||
| Images |  1307.gif (97.2 KB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1307 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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