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Expansion Intermediates of the Bacteriophage phi6 Procapsid
by single particle (icosahedral) reconstruction, at 20 A resolution
#1: Surface view with section colored by density value, Surface level: 1.5, Made by UCSF CHIMERA
#2: Surface view colored by radius, Surface level: 1.5, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 5356 |
|---|---|
| Authors | Nemecek D, Cheng N, Qiao J, Mindich L, Steven AC, Heymann JB |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 1.5, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 1.5, 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. 414, Issue 2, Page 260-71, Year 2011 |
|---|---|
| Title | Stepwise expansion of the bacteriophage ϕ6 procapsid: possible packaging intermediates. |
| Authors | Daniel Nemecek, Naiqian Cheng, Jian Qiao, Leonard Mindich, Alasdair C Steven, J Bernard Heymann National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA. |
| Keywords |  Bacteriophages (chemistry), Calorimetry, Differential Scanning, Capsid (chemistry), Cryoelectron Microscopy, RNA, Viral (genetics), Virus Assembly |
| Links | PII: S0022-2836(11)01128-4, DOI: 10.1016/j.jmb.2011.10.004, PubMed: 22019738, PMC: PMC3223026 |
 Map | |||||||||||||||||||||||||
| File |  EMD-5356.map ( map file in CCP4 format, 70306 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 = 683.25916 A , B = 683.25916 A , C = 683.25916 A , alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X = 2.62792 A , Y = 2.62792 A , Z = 2.62792 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | This is expansion intermediate of the bacteriophage phi6 procapsid that was obtained by RNA release from already packaged capsids. | ||||||||||||||||||||||||
 Supplement | |
| FSC | |
| FSC |  |
|---|---|
 Sample | |
| Name | Expansion Intermediate 2 of the P1247 Procapsid of Bacteriophage phi6 |
|---|---|
| Number of Components | 4 |
| Oligomeric State | Icosahedral shell of P1 dimers with P2, P4 and P7 subunits |
| Theoretical Mass | 12.6 MDa |
| Component #1: virus - Bacteriophage phi6 | |
| Scientific name | Bacteriophage phi6 |
| Theoretical Mass | 12.6 MDa |
| Scientific Name of Species | Bacteriophage phi6 |
| Common Name of Species | Bacteriophage phi6 |
| Empty | Yes |
| Enveloped | Yes |
| Isolate | STRAIN |
| Class | OTHER |
| Natural Source | Host Species: Pseudomonas syringae (NCBI Taxonomy: 317) Host Category: BACTERIA(EUBACTERIA) |
| Shell | Diameter: 420 A Name Element: P1 T Number: 1 |
 Experiment | |
| Sample Preparation | |
| Specimen Conc | 10 mg/ml |
|---|---|
| Specimen Support Details | Quantifoil 2/2/400 mesh grid |
| Specimen State | particle |
| Buffer | Details: 10 mM potassium phosphate, 1 mM MgCl2, 100 mM NaCl pH: 7.5 |
| Vitrification | |
| Cryogen Name | ETHANE |
| Details | Vitrification instrument: Reichert - Jung KF80 |
| Humidity | 80 |
| Instrument | LEICA KF80 |
| Temperature | 93 Kelvin |
| Imaging | |
| Microscope | FEI/PHILIPS CM200FEG |
| Date | 23-SEP-2008 |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 120 kV |
| Electron Dose | 15 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 50000 X, Calibrated: 48327 X |
| Astigmatism | objective lens astigmatism was corrected at 100,000 times magnification |
| Nominal Cs | 2.0 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 700 nm - 2100 nm |
| Specimen Holder | |
| Holder | Gatan 626 ( GATAN LIQUID NITROGEN ) |
| Temperature | 93 Kelvin |
| Camera | |
| Detector | Kodak SO163 film |
| Image Acquisition | |
| Scanner | NIKON SUPER COOLSCAN 9000 |
| Number of Digital Images | 52 |
| Sampling Size | 6.35 microns |
| Quant Bit Number | 16 |
 Processing | |
| Method | single particle (icosahedral) reconstruction |
|---|---|
| 3 D reconstruction | |
| Algorithm | Fourier space projection matching and reconstruction |
| Software | Bsoft |
| CTF Correction | phase flip particle images |
| Resolution By Author | 20 A
|
| Resolution Method | FSC at 0.3 cut-off |
| Single Particle | |
| Details | class 2 of 3 from multi-reference alignment |
| Number of Projections | 558 |
| Applied Symmetry | I (icosahedral) |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-5356.xml (7.9 KB) | ||
|---|---|---|---|
| Map data | emd_5356.map.gz (62.6 MB) | ||
| FSC (resolution estimation) | emd_5356_fsc.xml (4.2 KB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5356 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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