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DE NOVO MODEL OF BACTERIOPHAGE P22 PROCAPSID COAT PROTEIN
by single particle reconstruction, at 3.8 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-1824, Made by Jmol
#6: Superimposing with EM 3D map: EMDB-1824, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | PORTEIN DATA BANK (PDB) / 2xyy |
|---|---|
| Title | DE NOVO MODEL OF BACTERIOPHAGE P22 PROCAPSID COAT PROTEIN |
| Descriptor | COAT PROTEIN |
| Keywords |  VIRUS, ICOSAHEDRAL RECONSTRUCTION |
| Authors | Chen, D.-H., Baker, M.L., Hryc, C.F., Dimaio, F., Jakana, J., Wu, W., Dougherty, M., Haase-Pettingell, C., Schmid, M.F., Jiang, W., Baker, D., King, J.A., Chiu, W. |
| Date | Deposition: 2010-11-19, Release: 2011-02-02 |
| 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-1824, Made by Jmol #6: Superimposing with EM 3D map: EMDB-1824, 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 | Proc. Natl. Acad. Sci. U.S.A., Vol. 108, Issue 4, Page 1355-60, Year 2011 |
|---|---|
| Title | Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus. |
| Authors | Dong-Hua Chen, Matthew L Baker, Corey F Hryc, Frank DiMaio, Joanita Jakana, Weimin Wu, Matthew Dougherty, Cameron Haase-Pettingell, Michael F Schmid, Wen Jiang, David Baker, Jonathan A King, Wah Chiu National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA. |
| Keywords | Bacteriophage P22 (genetics), Binding Sites, Capsid (chemistry), Capsid Proteins (chemistry), Cryoelectron Microscopy, DNA Viruses (genetics), Models, Molecular, Protein Binding, Protein Conformation, Protein Structure, Tertiary, VP3 protein, Bluetongue virus, Viral Core Proteins, Viral Proteins (chemistry), Virion (genetics), Virus Assembly |
| Links | DOI: 10.1073/pnas.1015739108, PubMed: 21220301, PMC: PMC3029737 |
 Components | |
| ID 1 : P22 | |
| Image |   |
|---|---|
| Description | COAT PROTEIN |
| Type | polymer |
| Formula weight | 46796.133 Da |
| Number of molecules | 7 |
| Source | Method: Isolated from a genetically manipulated source Gene: 97540, ID:10754, ENTEROBACTERIA PHAGE P22Host: ID:90371, SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM, DB7136, 13AMH101 |
| Links | UniProt: A8CGC7, Sequence view |
 Sample | |
| Assembly | |
| Aggregation state | PARTICLE |
|---|---|
| Details | BAD MICROGRAPHS WERE EXCLUDED VISUALLY |
| Name | BACTERIOPHAGE P22 PROCAPSID |
| Buffer | |
| Name | 50 MM TRIS PH 7.6, 25 MM NACL, 2MM EDTA |
| Experiment | |
| Reconstruction method | SINGLE PARTICLE |
| Specimen type | VITREOUS ICE |
| Sample preparation | |
| pH | 7.6 |
| Sample concentration | 1.0 mg/ml |
| Sample support | |
| Details | HOLEY CARBON |
| Vitrification | |
| Details | VITRIFICATION 1 - CRYOGEN- ETHANE, HUMIDITY- 95, TEMPERATURE- 4.2, INSTRUMENT- VITROBOT, METHOD- BLOT FOR 2 SECONDS BEFORE PLUNGING, |
 Electron Microscopy | |
| Imaging | |
| Microscope | model: JEOL KYOTO-3000SFF |
|---|---|
| Date | 2008-03-07 |
| Electron gun | |
| Electron source | FIELD EMISSION GUN |
| Accelerating voltage | 300 kV |
| Electron dose | 36 e/A**2 |
| Illumination mode | FLOOD BEAM |
| Lens | |
| Mode | BRIGHT FIELD |
| Magnification | calibrated: 60000 X, nominal: 60000 X |
| Cs | nominal: 1.6 mm |
| Nominal defocus | max: 2800 nm, min: 500 nm |
| Specimen holder | |
| Temperature | 4.2 Kelvin |
| Detector | |
| Type | KODAK SO163 FILM |
| Image scans | |
| Number digital images | 921 |
 Processing | |
| 2D projection selection | |
| Number of particles | 23400 |
|---|---|
| Software name | EMAN |
| 3D reconstruction | |
| Actual pixel size | 1.06 A/pix |
| CTF correction method | EACH PARTICLE |
| Details | MAKE3D IN EMAN.N-TERMINAL 9 RESIDUES AND C-TERMINAL 5 RESIDUES WERE NOT MODELED.SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1824. |
| Method | FOURIER METHODS |
| Nominal pixel size | 1.06 A/pix |
| Resolution | 3.8 A |
| 3D fitting | |
| Refinement Protocol | EM |
| Refinement Space | REAL |
| Target criteria | FSC |
| Refine | |
| Ls d res high | 3.80 A |
| ID | 1 |
| Refine hist | |
| D res high | 3.80 |
| Total atoms | 2912 |
| Protein atoms | 2912 |
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