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The structure of JC polyomavirus (pH 7.4)
by single particle (icosahedral) reconstruction, at 19.0 A resolution
#1: Surface view with section colored by density value, Surface level: 43, Made by UCSF CHIMERA
#2: Surface view colored by radius, Surface level: 43, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 5183 |
|---|---|
| Title | The structure of JC polyomavirus (pH 7.4) |
| Map | Cryo-EM reconstruction of JC polyomavirus (pH 7.4) |
| Sample | JC polyomavirus in buffer A (pH 7.4) |
| Keywords |  JC, JCV, polyomavirus |
| Authors | Shen PS, Enderlein D, Nelson C, Carter WS, Kawano M, Xing L, Swenson RD, Olson NH, Baker TS, Cheng RH, Atwood WJ, Johne R, Belnap DM |
| Date | Deposition: 2010-04-12, Header release: 2010-12-08, Map release: 2011-01-19, Last update: 2011-09-23 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 43, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 43, 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 | Virology, Vol. 411, Issue 1, Page 142-52, Year 2011 |
|---|---|
| Title | The structure of avian polyomavirus reveals variably sized capsids, non-conserved inter-capsomere interactions, and a possible location of the minor capsid protein VP4. |
| Authors | Peter S Shen, Dirk Enderlein, Christian D S Nelson, Weston S Carter, Masaaki Kawano, Li Xing, Robert D Swenson, Norman H Olson, Timothy S Baker, R Holland Cheng, Walter J Atwood, Reimar Johne, David M Belnap Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA. |
| Keywords | Animals, Capsid (ultrastructure), Capsid Proteins (metabolism), Cryoelectron Microscopy, Macromolecular Substances (ultrastructure), Melopsittacus (virology), Polyomavirus (isolation & purification) |
| Links | DOI: 10.1016/j.virol.2010.12.005, PubMed: 21239031, PMC: PMC3057058 |
 Map | |||||||||||||||||||||||||
| File |  EMD-5183.map ( map file in CCP4 format, 197725 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= B= C: 597.78 A Alpha=beta=gamma: 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X= Y= Z: 1.62 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | Cryo-EM reconstruction of JC polyomavirus (pH 7.4) | ||||||||||||||||||||||||
 Supplement |
 Sample | |
| Name | JC polyomavirus in buffer A (pH 7.4) |
|---|---|
| Number of Components | 1 |
| Oligomeric State | virions |
| Component #1: virus - JCV | |
| Scientific name | JC polyomavirus |
| Common Name | JCV |
| Details | Cryo-EM of JC polyomavirus over holey carbon grids |
| Scientific Name of Species | JC polyomavirus |
| Common Name of Species | JCV |
| NCBI taxonomy | 10632 |
| Empty | No |
| Enveloped | No |
| Isolate | STRAIN |
| Class | VIRION |
| Natural Source | NCBI taxonomy: 9606 Host Species: Homo sapiens Host Category: VERTEBRATES |
| Shell | Id: 1 , Diameter: 5000 A, Name Element: VP1 , T Number: 7 |
 Experiment | |
| Sample Preparation | |
| Specimen Conc | 1.5 mg/ml |
|---|---|
| Specimen Support Details | 200 mesh copper grid (holey carbon) |
| Specimen State | particle |
| Buffer | Details: 10 mM Tris, 50 mM NaCl, 0.01 mM CaCl2 pH: 7.4 |
| Vitrification | |
| Method | 3 second blot before plunging |
| Cryogen Name | ETHANE |
| Details | Vitrification instrument: Vitrobot. vitrification carried out in nitrogen atmosphere |
| Humidity | 100 |
| Instrument | FEI VITROBOT |
| Temperature | 89 Kelvin |
| Imaging | |
| Microscope | FEI TECNAI F30 |
| Date | 23-APR-2007 |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 200 kV |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 39000, Calibrated: 39000 |
| Astigmatism | astigmatism was corrected at 59,000 times magnification |
| Nominal Cs | 2 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 500 nm - 4900 nm |
| Specimen Holder | |
| Holder | Side entry liquid nitrogen-cooled cryo specimen holder |
| Model | GATAN LIQUID NITROGEN |
| Temperature | 90 K ( 88 - 95 K) |
| Camera | |
| Detector | Kodak SO163 film |
| Image Acquisition | |
| Scanner | NIKON SUPER COOLSCAN 9000 |
| Number of Digital Images | 50 |
| Sampling Size | 6.35 |
| Quant Bit Number | 16 |
| Details | Micrographs digitized in positive contrast mode. |
 Processing | |
| Method | single particle (icosahedral) reconstruction |
|---|---|
| 3D reconstruction | |
| Algorithm | common lines |
| Software | PFT2 and EM3DR2 |
| CTF Correction | each micrograph |
| Resolution By Author | 19 A |
| Resolution Method | FSC at 0.3 cut-off |
| Single Particle | |
| Applied Symmetry | I (icosahedral) |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-5183.xml (7.8 KB) | ||
|---|---|---|---|
| Map data | emd_5183.map.gz (91.1 MB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5183 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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