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CryoEM structure of cytoplasmic polyhedrosis virus
by single particle (icosahedral) reconstruction, at 3.9 A resolution
#1: Surface view with section colored by density value, Surface level: 3, Made by UCSF CHIMERA
#2: Surface view colored by radius, Surface level: 3, Made by UCSF CHIMERA
#3: Simplified surface model with fitted atomic model: PDB-3iz3, Made by Jmol
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 5233 |
|---|---|
| Title | CryoEM structure of cytoplasmic polyhedrosis virus |
| Map | This is a hemi-spherical density map of threefold view of cytoplasmic polyhedrosis virus |
| Sample | Cytoplasmic Polyhedrosis Virus |
| Keywords |  cryoelectron microscopy |
| Authors | Cheng L, Sun J, Zhang K, Mou Z, Huang X, Ji G, Sun F, Zhang J, Zhu P |
| Date | Deposition: 2010-09-14, Header release: 2011-03-10, Map release: 2011-03-10, Last update: 2012-04-02 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 3, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 3, Made by UCSF CHIMERA #3: Simplified surface model with fitted atomic model: PDB-3iz3, 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 1373-8, Year 2011 |
|---|---|
| Title | Atomic model of a cypovirus built from cryo-EM structure provides insight into the mechanism of mRNA capping. |
| Authors | Lingpeng Cheng, Jingchen Sun, Kai Zhang, Zongjun Mou, Xiaoxing Huang, Gang Ji, Fei Sun, Jingqiang Zhang, Ping Zhu National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China. |
| Keywords | Amino Acid Sequence, Capsid (metabolism), Capsid Proteins (chemistry), Cryoelectron Microscopy (methods), Models, Molecular, Models, Structural, Molecular Sequence Data, Molecular Structure, Protein Conformation, Protein Structure, Secondary, Protein Structure, Tertiary, RNA Caps, RNA, Messenger (genetics), RNA, Viral (genetics), Reoviridae (genetics), Sequence Homology, Amino Acid |
| Links | DOI: 10.1073/pnas.1014995108, PubMed: 21220303, PMC: PMC3029759 |
 Map | |||||||||||||||||||||||||
| File |  EMD-5233.map ( map file in CCP4 format, 819202 KB ) | ||||||||||||||||||||||||
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| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
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| Data Type | Image stored as Reals | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
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| Unit Cell | A: 761.60004 A, B: 761.60004 A, C: 595 A Alpha=beta=gamma: 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X= Y= Z: 1.19 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | This is a hemi-spherical density map of threefold view of cytoplasmic polyhedrosis virus | ||||||||||||||||||||||||
 Supplement |
 Sample | |
| Name | Cytoplasmic Polyhedrosis Virus |
|---|---|
| Number of Components | 5 |
| Component #1: virus - CPV | |
| Scientific name | Cypovirus |
| Common Name | CPV |
| Scientific Name of Species | Cypovirus |
| Common Name of Species | CPV |
| NCBI taxonomy | 10981 |
| Empty | No |
| Enveloped | No |
| Isolate | STRAIN |
| Class | VIRION |
| Natural Source | NCBI taxonomy: 7091 Host Species: Bombyx mori Host Category: INVERTEBRATES |
| Shell | Id: 1 , Diameter: 720 A, T Number: 1 |
 Experiment | |
| Sample Preparation | |
| Specimen Support Details | 200 mesh |
|---|---|
| Specimen State | particle |
| Buffer | pH: 7.5 |
| Vitrification | |
| Method | Blot for 4 seconds before plunging |
| Cryogen Name | ETHANE |
| Humidity | 100 |
| Instrument | FEI VITROBOT |
| Imaging | |
| Microscope | FEI TITAN KRIOS |
| Date | 10-APR-2010 |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 300 kV |
| Electron Dose | 20 e/A**2 |
| Illumination Mode | OTHER |
| Lens | |
| Magnification | Calibrated: 75000 |
| Nominal Cs | 2.7 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 800 nm - 2800 nm |
| Specimen Holder | |
| Model | OTHER |
| Camera | |
| Detector | Gatan 4kx4K CCD |
| Image Acquisition | |
| Number of Digital Images | 1600 |
| Sampling Size | 1.19 |
| Quant Bit Number | 24 |
 Processing | |
| Method | single particle (icosahedral) reconstruction |
|---|---|
| 3D reconstruction | |
| Algorithm | cross-common lines |
| Software | IMIRS |
| CTF Correction | Each micrograph |
| Resolution By Author | 3.9 A |
| Resolution Method | FSC 0.143 |
| Single Particle | |
| Number of Projections | 29000 |
| Applied Symmetry | I (icosahedral) |
| Atomic Model Fitting | |
| Fitted Coordinate | |
| PDB entry ID | |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-5233.xml (6.8 KB) | ||
|---|---|---|---|
| Map data | emd_5233.map.gz (672.2 MB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5233 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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| movie #3 |
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