3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
The structure of PBCV-1 (local symmetry averaged map of major capsid protein)
by single particle reconstruction, at 9.8 A resolution
#1: Surface view. , Surface level: 1.5, Made by UCSF CHIMERA
#2: Surface view colored by radius, Surface level: 1.5, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 5385 |
|---|---|
| Title | The structure of PBCV-1 (local symmetry averaged map of major capsid protein) |
| Map | Local symmetry averaged map of major capsid protein of PBCV-1 (within a trisymmetron) |
| Sample | PBCV-1 |
| Keywords |  Cell entry, minor protein, double jelly-roll |
| Authors | Zhang XZ, Xiang Y, Dunigan DD, Klose T, Chipman PR, Etten JLV, Rossmann MG |
| Date | Deposition: 2012-01-12, Header release: 2012-06-28, Map release: 2012-06-28, Last update: 2012-06-28 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view. , Surface level: 1.5, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 1.5, 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 | Proc. Natl. Acad. Sci. U.S.A., Vol. 108, Issue 36, Page 14837-42, Year 2011 |
|---|---|
| Title | Three-dimensional structure and function of the Paramecium bursaria chlorella virus capsid. |
| Authors | Xinzheng Zhang, Ye Xiang, David D Dunigan, Thomas Klose, Paul R Chipman, James L Van Etten, Michael G Rossmann Department of Biological Sciences, Purdue University, 240 South Martin Jischke Drive, West Lafayette, IN 47907-2032, USA. |
| Keywords | Capsid (chemistry), Chlorella (virology), Phycodnaviridae (chemistry), Protein Structure, Quaternary, Viral Proteins (chemistry), Virus Assembly (physiology), Virus Release (physiology) |
| Links | DOI: 10.1073/pnas.1107847108, PubMed: 21873222, PMC: PMC3169150 |
 Map | |||||||||||||||||||||||||
| File |  EMD-5385.map ( map file in CCP4 format, 4002 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: 192 A Alpha=beta=gamma: 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X= Y= Z: 1.92 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | Local symmetry averaged map of major capsid protein of PBCV-1 (within a trisymmetron) | ||||||||||||||||||||||||
 Supplement |
 Sample | |
| Name | PBCV-1 |
|---|---|
| Number of Components | 8 |
| Component #1: virus - PBCV-1 | |
| Scientific name | Paramecium bursaria Chlorella virus 1 |
| Common Name | PBCV-1 |
| Scientific Name of Species | Paramecium bursaria Chlorella virus 1 |
| Common Name of Species | PBCV-1 |
| NCBI taxonomy | 10506 |
| Empty | No |
| Enveloped | Yes |
| Isolate | STRAIN |
| Class | VIRION |
| Natural Source | NCBI taxonomy: 554065 Host Species: Chlorella variabilis Host Category: ALGAE |
| Shell | Id: 1 , Diameter: 1850 A, Name Element: VP54 |
 Experiment | |
| Sample Preparation | |
| Specimen Conc | 1 mg/ml |
|---|---|
| Specimen Support Details | 200 mesh grid |
| Specimen State | particle |
| Buffer | Details: BBM pH: 7 |
| Vitrification | |
| Cryogen Name | ETHANE |
| Humidity | 85 |
| Instrument | NONE |
| Temperature | 174 Kelvin |
| Imaging | |
| Microscope | FEI/PHILIPS CM300FEG/T |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 300 kV |
| Illumination Mode | OTHER |
| Lens | |
| Magnification | Nominal: 33000, Calibrated: 33065 |
| Astigmatism | objective lens astigmatism was corrected at 250,000 times magnification |
| Nominal Cs | 2 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 1000 nm - 4000 nm |
| Specimen Holder | |
| Holder | Single tilt holder |
| Model | GATAN LIQUID NITROGEN |
| Temperature | 175 K |
| Camera | |
| Detector | Kodak SO163 film |
| Image Acquisition | |
| Number of Digital Images | 800 |
| Sampling Size | 6.75 |
| Quant Bit Number | 16 |
 Processing | |
| Method | single particle reconstruction |
|---|---|
| 3D reconstruction | |
| Algorithm | EMAN routine |
| Software | EMAN |
| CTF Correction | Each micrograph |
| Resolution By Author | 9.8 A |
| Resolution Method | FSC at 0.5 cut-off |
| Single Particle | |
| Number of Projections | 17016 |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-5385.xml (7 KB) | ||
|---|---|---|---|
| Map data | emd_5385.map.gz (378.9 KB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5385 | ||
| Movie files | |||
| movie #1 |
| ||
| movie #2 |
| ||
Top
Gallery
List
Diagram
Statistics
Documents
PDBj
EM Navigator
Detail page - EMDB-5385
Z (Sec.)
Y (Row.)
X (Col.)
Contact