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Capsid structure and its Stability at the Late Stages of Bacteriophage SPP1 Assembly
by single particle (icosahedral) reconstruction, at 10.5 A resolution
#1: Surface view with section colored by density value, Surface level: 8, Made by UCSF CHIMERA
#2: Surface view colored by radius, Surface level: 8, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 2052 |
|---|---|
| Authors | White HE, Sherman MB, Brasiles S, Jacquet E, Seavers P, Tavares P, Orlova EV |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 8, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 8, 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. 86, Issue 12, Page 6768-77, Year 2012 |
|---|---|
| Title | Capsid structure and its stability at the late stages of bacteriophage SPP1 assembly. |
| Authors | Helen E White, Michael B Sherman, Sandrine Brasilès, Eric Jacquet, Philippa Seavers, Paulo Tavares, Elena V Orlova Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, London, United Kingdom. |
| Keywords |  Bacteriophages (chemistry), Capsid (chemistry), Capsid Proteins (chemistry), Cryoelectron Microscopy, Models, Molecular, Protein Stability, Virus Assembly |
| Links | DOI: 10.1128/JVI.00412-12, PubMed: 22514336, PMC: PMC3393595 |
 Map | |||||||||||||||||||||||||
| File |  EMD-2052.map ( map file in CCP4 format, 536872 KB ) | ||||||||||||||||||||||||
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| Projections & Slices | Size of images:
Images are generated by Spider package. (generated in cubic-lattice coordinate) | ||||||||||||||||||||||||
| Density |
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| Data Type | Image stored as Reals | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
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| Unit Cell | A = 894.60004 A , B = 894.0 A , C = 894.0 A , alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X = 1.491 A , Y = 1.49 A , Z = 1.49 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | Reconstruction of an SPP1 capsid after DNA ejection | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | Capsid of SPP1 |
|---|---|
| Number of Components | 1 |
| Oligomeric State | Icosahedron |
| Component #1: virus - Bacillus phage SPP1 | |
| Scientific name | Bacillus phage SPP1 |
| Scientific Name of Species | Bacillus phage SPP1 (NCBI Taxonomy: 10724) |
| Empty | Yes |
| Enveloped | No |
| Isolate | SPECIES |
| Class | OTHER |
| Natural Source | Host Species: Bacillus subtilis (NCBI Taxonomy: 1423) Host Category: BACTERIA(EUBACTERIA) |
| Shell | Diameter: 600 A T Number: 7 |
 Experiment | |
| Sample Preparation | |
| Specimen Support Details | holey carbon film grids |
|---|---|
| Specimen State | particle |
| Vitrification | |
| Cryogen Name | ETHANE |
| Instrument | FEI VITROBOT MARK I |
| Imaging | |
| Microscope | JEOL 2200FS |
| Date | 06-APR-2005 |
| Details | Low-dose imaging procedure |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 200 kV |
| Electron Dose | 20 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 50000 X, |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder | |
| Holder | ( GATAN LIQUID NITROGEN ) |
| Camera | |
| Detector | Kodak SO163 film |
| Image Acquisition | |
| Scanner | ZEISS SCAI |
| Number of Digital Images | 94 |
| Sampling Size | 7 microns |
 Processing | |
| Method | single particle (icosahedral) reconstruction |
|---|---|
| 3 D reconstruction | |
| Algorithm | Angular reconstitution |
| Software | Imagic |
| CTF Correction | Phase flipping |
| Resolution By Author | 10.5 |
| Resolution Method | FSC at 0.5 cut-off |
| Single Particle | |
| Number of Projections | 1200 |
| Applied Symmetry | I (icosahedral) |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-2052.xml (6.4 KB) | ||
|---|---|---|---|
| Map data | emd_2052.map.gz (119 MB) | ||
| Images |  EMD-2052.jpg (226.5 KB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2052 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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