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Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus
by single particle (icosahedral) reconstruction, at 4.0 A resolution
#1: Surface view with section colored by density value, Surface level: 0.4, Made by UCSF CHIMERA
#2: Surface view colored by radius, Surface level: 0.4, Made by UCSF CHIMERA
#3: Surface view with fitted model, atomic models: PDB-2xyz, Surface level: 0.4, Made by UCSF CHIMERA
#4: Simplified surface model with fitted atomic model: PDB-2xyz, Made by Jmol
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 1826 |
|---|---|
| Title | Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus |
| Map | This is the icosahedral density map for bacteriophage P22 virion solved by cryo-EM at 4.0-Angstrom resolution |
| Sample | Bacteriophage P22 virion |
| Keywords |  bacteriophage, phage, P22, virion, icosahedral reconstruction, backbone, maturation, dsDNA virus |
| Authors | Chen D-H, Baker ML, Hryc CF, DiMaio F, Jakana J, Wu W, Dougherty M, Haase-Pettingell C, Schmid MF, Jiang W, Baker D, King JA, Chiu W |
| Date | Deposition: 2010-11-19, Header release: 2010-12-10, Map release: 2011-01-28, Last update: 2011-01-28 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 0.4, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 0.4, Made by UCSF CHIMERA #3: Surface view with fitted model, atomic models: PDB-2xyz, Surface level: 0.4, Made by UCSF CHIMERA #4: Simplified surface model with fitted atomic model: PDB-2xyz, Made by Jmol |
| Supplemental images | |
| Structure viewers |  Yorodumi,  Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article Fit: output model 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 |
 Map | |||||||||||||||||||||||||
| File |  EMD-1826.map ( map file in CCP4 format, 2529356 KB ) | ||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
| ||||||||||||||||||||||||
| Data Type | Image stored as Reals | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
| ||||||||||||||||||||||||
| Unit Cell | A= B= C: 915.84 A Alpha=beta=gamma: 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X= Y= Z: 1.06 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | This is the icosahedral density map for bacteriophage P22 virion solved by cryo-EM at 4.0-Angstrom resolution | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | Bacteriophage P22 virion |
|---|---|
| Number of Components | 1 |
| Details | This sample is infectious P22 virion filled with DNA and having a protruding tail, but the capsid shell has icosahedral symmetry |
| Component #1: virus - P22 | |
| Scientific name | Enterobacteria phage P22 |
| Common Name | P22 |
| Scientific Name of Species | Enterobacteria phage P22 |
| Common Name of Species | P22 |
| NCBI taxonomy | 10754 |
| Empty | No |
| Enveloped | No |
| Isolate | STRAIN |
| Class | VIRION |
| Natural Source | NCBI taxonomy: 90371 Host Species: Salmonella enterica subsp. enterica serovar Typhimurium Host Category: BACTERIA(EUBACTERIA) |
| Shell | Id: 1 , Diameter: 710 A, T Number: 7 |
 Experiment | |
| Sample Preparation | |
| Specimen Conc | 1 mg/ml |
|---|---|
| Specimen Support Details | 400 mesh copper grid |
| Specimen State | particle |
| Buffer | Details: 50 mM Tris pH 7.6, 25 mM NaCl pH: 7.6 |
| Vitrification | |
| Method | Blot for 2 seconds before plunging |
| Cryogen Name | ETHANE |
| Details | Vitrification instrument: Vitrobot |
| Humidity | 95 |
| Instrument | FEI VITROBOT |
| Temperature | 4.2 Kelvin |
| Imaging | |
| Microscope | JEOL 3000SFF |
| Date | 06-DEC-2005 |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 300 kV |
| Electron Dose | 36 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 60000, Calibrated: 60000 |
| Astigmatism | Objective lens astigmatism was corrected at 400,000 times magnification |
| Nominal Cs | 1.6 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 300 nm - 2300 nm |
| Specimen Holder | |
| Holder | Top entry |
| Model | JEOL |
| Temperature | 4.2 K ( 4.2 - 4.2 K) |
| Camera | |
| Detector | Kodak SO163 film |
| Image Acquisition | |
| Scanner | NIKON SUPER COOLSCAN 9000 |
| Number of Digital Images | 382 |
| Sampling Size | 6.35 |
| Quant Bit Number | 8 |
 Processing | |
| Method | single particle (icosahedral) reconstruction |
|---|---|
| 3D reconstruction | |
| Algorithm | Fourier methods |
| Euler Angles Details | EMAN:az, alt, phi |
| Software | EMAN |
| CTF Correction | Each particle |
| Resolution By Author | 4 A |
| Resolution Method | FSC at 0.5 cut-off |
| Single Particle | |
| Details | The particles were selected using an automatic selection program |
| Number of Projections | 18300 |
| Applied Symmetry | I (icosahedral) |
| Atomic Model Fitting | |
| Fitted Coordinate | |
| PDB entry ID | |
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