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CryoEM map of the mature astrovirus (HAstV-1)
by single particle (icosahedral) reconstruction, at 25 A resolution
#1: Surface view with section colored by density value, Surface level: 55, Made by UCSF CHIMERA
#2: Surface view colored by radius, Surface level: 55, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 5413 |
|---|---|
| Authors | Dryden KA, Tihova M, Nowotny N, Matsui SM, Mendez E, Yeager M |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 55, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 55, 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-5413.map ( map file in CCP4 format, 63255 KB ) | ||||||||||||||||||||||||
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| 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 = 502.0 A , B = 502.0 A , C = 502.0 A , alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X = 2 A , Y = 2 A , Z = 2 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | Reconstruction of mature human astrovirus HAstV-1 | ||||||||||||||||||||||||
 Supplement |
 Sample | |
| Name | mature human astrovirus HAstV-1 |
|---|---|
| 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 | Host Species: Homo sapiens (NCBI Taxonomy: 9606) Host Category: VERTEBRATES |
| Shell | Diameter: 440 A T Number: 3 |
 Experiment | |
| Sample Preparation | |
| Specimen Support Details | holey carbon, glow discharged with amylamine |
|---|---|
| Specimen State | particle |
| Buffer | Details: 50mM Tris-HCl, pH 8, 100mM NaCl, 10mM MgCl2, 10mM CaCl2 |
| Vitrification | |
| Method | watch drop spread on filter paper before plunging |
| Cryogen Name | ETHANE |
| Instrument | HOMEMADE PLUNGER |
| Imaging | |
| Microscope | FEI/PHILIPS CM120T |
| Date | 22-SEP-1997 |
| Electron Gun | |
| Electron Source | LAB6 |
| Accelerating Voltage | 120 kV |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 35000 X, |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 1450 nm - 1850 nm |
| Specimen Holder | |
| Holder | ( GATAN LIQUID NITROGEN ) |
| Camera | |
| Detector | Kodak SO-163 film |
| Image Acquisition | |
| Scanner | ZEISS SCAI |
| Number of Digital Images | 6 |
| Sampling Size | 7 microns |
 Processing | |
| Method | single particle (icosahedral) reconstruction |
|---|---|
| 3 D reconstruction | |
| Algorithm | polar Fourier transform |
| Software | Auto3dem |
| Resolution By Author | 25 |
| Resolution Method | FSC at 0.5 cut-off |
| Single Particle | |
| Details | Particles were selected with X3D, and processed with Auto3dem. |
| Number of Projections | 397 |
| Applied Symmetry | I (icosahedral) |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-5413.xml (6.6 KB) | ||
|---|---|---|---|
| Map data | emd_5413.map.gz (22.3 MB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5413 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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