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Capsid structure of the infectious Prochlorococcus Cyanophage P-SSP7
by single particle reconstruction, at 4.6 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-1713, Made by Jmol
#6: Superimposing with EM 3D map: EMDB-1713, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | PORTEIN DATA BANK (PDB) / 2xd8 |
|---|---|
| Title | Capsid structure of the infectious Prochlorococcus Cyanophage P-SSP7 |
| Descriptor | T7-LIKE CAPSID PROTEIN |
| Keywords |  VIRUS, MARINE PODOVIRUS, T7-LIKE VIRUS |
| Authors | Liu, X., Zhang, Q., Murata, K., Baker, M.L., Sullivan, M.B., Fu, C., Dougherty, M., Schmid, M.F., Osburne, M.S., Chisholm, S.W., Chiu, W. |
| Date | Deposition: 2010-04-30, Release: 2010-06-16 |
| 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-1713, Made by Jmol #6: Superimposing with EM 3D map: EMDB-1713, 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 | Nat. Struct. Mol. Biol., Vol. 17, Issue 7, Page 830-6, Year 2010 |
|---|---|
| Title | Structural changes in a marine podovirus associated with release of its genome into Prochlorococcus. |
| Authors | Xiangan Liu, Qinfen Zhang, Kazuyoshi Murata, Matthew L Baker, Matthew B Sullivan, Caroline Fu, Matthew T Dougherty, Michael F Schmid, Marcia S Osburne, Sallie W Chisholm, Wah Chiu National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, Texas, USA. |
| Keywords | Capsid (chemistry), Genome, Viral, Models, Molecular, Podoviridae (chemistry), Prochlorococcus (virology), Viral Proteins (chemistry), Virion (chemistry) |
| Links | DOI: 10.1038/nsmb.1823, PubMed: 20543830, PMC: PMC2924429 |
 Components | |
| ID 1 : GP10 | |
| Image |   |
|---|---|
| Description | T7-LIKE CAPSID PROTEIN |
| Type | polymer |
| Formula weight | 39494.582 Da |
| Number of molecules | 7 |
| Source | Method: Isolated from a genetically manipulated source Description: P-SSP7 WERE PROPAGATED ON PROCHLOROCOCCUS MED4. Gene: ID:268748, PROCHLOROCOCCUS PHAGE P-SSP7Host: ID:1220, PROCHLOROCOCCUS MED4 |
| Links | UniProt: Q58N30, Sequence view |
 Sample | |
| Assembly | |
| Aggregation state | PARTICLE |
|---|---|
| Name | CYANOPHAGE P-SSP7 |
| Buffer | |
| Name | 100 MM TRIS-HCL, 100 MM MGSO4, AND 30 MM NACL |
| Experiment | |
| Reconstruction method | SINGLE PARTICLE |
| Specimen type | VITREOUS ICE |
| Sample preparation | |
| pH | 7.5 |
| Sample concentration | 5.0 mg/ml |
| Sample support | |
| Details | HOLEY CARBON |
 Electron Microscopy | |
| Imaging | |
| Microscope | model: OTHER |
|---|---|
| Date | 2007-08-31 |
| Electron gun | |
| Electron source | FIELD EMISSION GUN |
| Accelerating voltage | 300 kV |
| Electron dose | 20 e/A**2 |
| Illumination mode | LOW DOSE |
| Lens | |
| Mode | BRIGHT FIELD |
| Magnification | nominal: 60000 X |
| Cs | nominal: 4.1 mm |
| Nominal defocus | max: 3000 nm, min: 600 nm |
| Specimen holder | |
| Temperature | 101 Kelvin |
| Detector | |
| Type | KODAK SO163 FILM |
| Image scans | |
| Number digital images | 1059 |
 Processing | |
| 2D projection selection | |
| Number of particles | 36000 |
|---|---|
| Software name | MPSA |
| 3D reconstruction | |
| Actual pixel size | 1.17 A/pix |
| CTF correction method | INDIVIDUAL MICROGRAPH |
| Details | SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1713. |
| Magnification calibration | 2D CRYSTAL |
| Method | CROSS-COMMON LINES |
| Nominal pixel size | 1.27 A/pix |
| Resolution | 4.6 A |
| 3D fitting list | |
| PDB entry ID | 1IJG, 2JES |
| Refine | |
| Ls d res high | 4.60 A |
| ID | 1 |
| Refine hist | |
| D res high | 4.60 |
| Total atoms | 2541 |
| Protein atoms | 2541 |
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