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CryoEM map of the immature human astrovirus HAstV-8
by single particle (icosahedral) reconstruction, at 25 A resolution
#1: Surface view with section colored by density value, Surface level: 0.85, Made by UCSF CHIMERA
#2: Surface view colored by radius, Surface level: 0.85, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 5414 |
|---|---|
| Title | CryoEM map of the immature human astrovirus HAstV-8 |
| Map | reconstruction of immature human astrovirus HAstV-8 |
| Sample | immature human astrovirus HAstV-8 |
| Keywords |  T=3 virus |
| Authors | Dryden KA, Tihova M, Nowotny N, Matsui SM, Mendez E, Yeager M |
| Date | Deposition: 2012-04-24, Header release: 2012-06-28, Map release: 2012-06-28, Last update: 2012-11-07 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 0.85, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 0.85, 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. Mol. Biol., Vol. 422, Issue 5, Page 650-8, Year 2012 |
|---|---|
| Title | Immature and mature human astrovirus: structure, conformational changes, and similarities to hepatitis E virus. |
| Authors | Kelly A Dryden, Mariana Tihova, Norbert Nowotny, Suzanne M Matsui, Ernesto Mendez, Mark Yeager Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA. |
| Keywords | Amino Acid Sequence, Cryoelectron Microscopy, Hepatitis E virus (ultrastructure), Humans, Image Processing, Computer-Assisted, Mamastrovirus (ultrastructure), Molecular Sequence Data, Sequence Alignment, Sequence Analysis, DNA, Virion (ultrastructure) |
| Links | PII: S0022-2836(12)00502-5, DOI: 10.1016/j.jmb.2012.06.029, PubMed: 22743104 |
 Map | |||||||||||||||||||||||||
| File |  EMD-5414.map ( map file in CCP4 format, 158609 KB ) | ||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
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| Data Type | Image stored as Reals | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
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| Unit Cell | A= B= C: 531.95996 A Alpha=beta=gamma: 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X= Y= Z: 1.56 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | reconstruction of immature human astrovirus HAstV-8 | ||||||||||||||||||||||||
 Supplement |
 Sample | |
| Name | immature human astrovirus HAstV-8 |
|---|---|
| Number of Components | 1 |
| Component #1: virus - Human astrovirus | |
| Scientific name | Human astrovirus |
| Scientific Name of Species | Human astrovirus |
| NCBI taxonomy | 12702 |
| Empty | No |
| Enveloped | No |
| Isolate | STRAIN |
| Class | VIRION |
| Natural Source | NCBI taxonomy: 9606 Host Species: Homo sapiens Host Category: VERTEBRATES |
| Shell | Id: 1 , Diameter: 440 A, T Number: 3 |
 Experiment | |
| Sample Preparation | |
| Specimen Support Details | glow discharged with amylamine |
|---|---|
| Specimen State | particle |
| Buffer | Details: 50mM Tris-HCl, pH 7.4, 100mM NaCl, 10mM EDTA |
| Vitrification | |
| Method | watch drop spread on filter paper before plunging |
| Cryogen Name | ETHANE |
| Instrument | HOMEMADE PLUNGER |
| Imaging | |
| Microscope | FEI/PHILIPS CM120T |
| Date | 22-DEC-2003 |
| Electron Gun | |
| Electron Source | LAB6 |
| Accelerating Voltage | 120 kV |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 45000 |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 1450 nm - 1850 nm |
| Specimen Holder | |
| Model | GATAN LIQUID NITROGEN |
| Camera | |
| Detector | Kodak SO-163 film |
| Image Acquisition | |
| Scanner | ZEISS SCAI |
| Number of Digital Images | 7 |
| Sampling Size | 7 |
 Processing | |
| Method | single particle (icosahedral) reconstruction |
|---|---|
| 3D reconstruction | |
| Algorithm | polar Fourier transform |
| Software | Auto3dem |
| Resolution By Author | 25 A |
| Resolution Method | FSC at 0.5 cut-off |
| Single Particle | |
| Details | Particles were boxed with X3D and processed with Auto3dem |
| Number of Projections | 451 |
| Applied Symmetry | I (icosahedral) |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-5414.xml (6.5 KB) | ||
|---|---|---|---|
| Map data | emd_5414.map.gz (22.3 MB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5414 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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