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Homology model of avian polyomavirus asymmetric unit
by single particle (icosahedral) reconstruction, at 11.3 A resolution
#1: Biological unit as complete icosahedral assembly, Made by Jmol
#2: Biological unit as icosahedral pentamer, Made by Jmol
#3: Biological unit as icosahedral 23 hexamer, Made by Jmol
#4: Depositted structure unit, Made by Jmol
#5: Superimposing with simplified surface model of EM map, EMDB-5180, Made by Jmol
#6: Superimposing with EM 3D map: EMDB-5180, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | PORTEIN DATA BANK (PDB) / 3iys |
|---|---|
| Title | Homology model of avian polyomavirus asymmetric unit |
| Descriptor | Major capsid protein VP1 |
| Keywords |  VIRUS, avian, polyomavirus, APV, icosahedral virus |
| Authors | Shen, P.S., Enderlein, D., Nelson, C.D.S., Carter, W.S., Kawano, M., Xing, L., Swenson, R.D., Olson, N.H., Baker, T.S., Cheng, R.H., Atwood, W.J., Johne, R., Belnap, D.M. |
| Date | Deposition: 2010-04-19, Release: 2011-01-26 |
| PDBj Mine pages |  Summary, Structural Details, Experimental Details, Functional Details |
| Other databases | RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST |
| Structure Visualization | |
| Movies |  Movie Page#1: Biological unit as complete icosahedral assembly, Made by Jmol #2: Biological unit as icosahedral pentamer, Made by Jmol #3: Biological unit as icosahedral 23 hexamer, Made by Jmol #4: Depositted structure unit, Made by Jmol #5: Superimposing with simplified surface model of EM map, EMDB-5180, Made by Jmol #6: Superimposing with EM 3D map: EMDB-5180, Made by UCSF CHIMERA |
| Structure viewers |  Yorodumi, jV4, Jmol,  Biological unit (Images, jV) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article Fit: target map of fitting |
| 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 |
 Components | |
| ID 1 : Major structural protein VP1 | |
| Image |   |
|---|---|
| Description | Major capsid protein VP1 |
| Type | polymer |
| Formula weight | 37449.703 Da |
| Number of molecules | 6 |
| Source | Method: Isolated from a natural source Common name: BFPyV NCBI taxonomy: ID:10625Organism scientific: Budgerigar fledgling disease polyomavirus |
| Links | UniProt: P13891, Sequence view |
 Sample | |
| Assembly | |
| Aggregation state | PARTICLE |
|---|---|
| Details | Cryo-EM single particle reconstruction |
| Name | avian polyomavirus |
| Virus entity | |
| Virus host category | vertebrates |
| Virus host species | avian |
| Virus isolate | SPECIES |
| Virus type | virion |
| Buffer | |
| Name | GP buffer with 250 mM L-arginine |
| Experiment | |
| Reconstruction method | SINGLE PARTICLE |
| Specimen type | VITREOUS ICE (CRYO EM) |
| Sample preparation | |
| pH | 10.7 |
| Sample support | |
| Details | avian polyomavirus in holey carbon grid |
| Vitrification | |
| Cryogen name | ETHANE |
| Details | APV |
| Humidity | 100% |
| Instrument | FEI vitrobot |
| Method | 3 second blot |
| Temp | 4.0 Kelvin |
 Electron Microscopy | |
| Imaging | |
| Date | 23-APR-2007 |
|---|---|
| Electron gun | |
| Accelerating voltage | 200 kV |
| Illumination mode | FLOOD BEAM |
| Lens | |
| Mode | BRIGHT FIELD |
| Magnification | calibrated: 39000 X, nominal: 39000 X |
| Astigmatism | astigmatism was corrected at 59,000 times magnification |
| Detector distance | 0.0 |
| Nominal defocus | max: 4900 nm, min: 500 nm |
| Specimen holder | |
| Specimen holder | model: GATAN LIQUID NITROGEN, type: Side entry liquid nitrogen-cooled cryo specimen holder |
| Tilt angle | min: 0.0 degrees, max: 0.0 degrees |
| Temperature | 90 Kelvin |
| Recording temperature | maximum: 95, minimum: 88 |
 Processing | |
| 2D projection selection | |
| Software name | UCSF Chimera |
|---|---|
| Single particle entity | |
| Symmetry type | ICOSAHEDRAL |
| 3D reconstruction | |
| Actual pixel size | 1.57 A/pix |
| CTF correction method | full CTF correction (FSC cutoff 0.3) |
| Magnification calibration | against simian virus 40 atomic coordinates |
| Method | Fourier Bessel |
| Nominal pixel size | 1.63 A/pix |
| Number of particles | 5338 |
| Resolution | 11.3 A |
| Software | PFT3DR |
| 3D fitting | |
| Method | rigid body |
| Refinement Protocol | rigid body |
| Refinement Space | REAL |
| Software name | UCSF Chimera |
| Target criteria | cross-correlation coefficient |
| Refine hist | |
| Total atoms | 2004 |
| Protein atoms | 2004 |
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