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3.88 Angstrom structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy
by single particle (icosahedral) reconstruction, at 3.880 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-1508, Made by Jmol
#6: Superimposing with EM 3D map: EMDB-1508, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | PORTEIN DATA BANK (PDB) / 3cnf |
|---|---|
| Title | 3.88 Angstrom structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy |
| Descriptor | VP1 VP3 |
| Keywords |  VIRUS, cytoplasmic polyhedrosis virus, capsid protein, turret protein, polyhedrin-binding domain, guanylyltransferase domain, icosahedral virus |
| Authors | Yu, X., Jin, L., Zhou, Z.H. |
| Date | Deposition: 2008-03-25, Release: 2008-04-29 |
| 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-1508, Made by Jmol #6: Superimposing with EM 3D map: EMDB-1508, 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 | Nature, Vol. 453, Issue 7193, Page 415-9, Year 2008 |
|---|---|
| Title | 3.88 A structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy. |
| Authors | Xuekui Yu, Lei Jin, Z Hong Zhou Department of Pathology and Laboratory Medicine, The University of Texas Medical School at Houston, Houston, Texas 77030, USA. |
| Keywords | Animals, Bombyx (virology), Capsid Proteins (chemistry), Cryoelectron Microscopy, Genome, Viral (physiology), Larva (virology), Models, Molecular, RNA Caps (genetics), RNA Transport, RNA, Viral (genetics), Reoviridae (chemistry) |
| Links | DOI: 10.1038/nature06893, PubMed: 18449192, PMC: PMC2746981 |
 Components | |
| ID 1 : VP1 | |
| Image |   |
|---|---|
| Description | VP1 |
| Type | polymer |
| Formula weight | 148561.656 Da |
| Number of molecules | 2 |
| Source | Method: Isolated from a natural source Organism scientific: Bombyx mori cypovirus 1 |
| Links | UniProt: Q6TS43, Sequence view |
| ID 2 : VP3 | |
| Image |   |
| Description | VP3 |
| Type | polymer |
| Formula weight | 119747.945 Da |
| Number of molecules | 1 |
| Source | Method: Isolated from a natural source Details: The cytoplasmic polyhedrosis virus was isolated and purified from infected Bombyx mori larvae. Organism scientific: Bombyx mori cypovirus 1 |
| Links | UniProt: Q9E957, Sequence view |
 Sample | |
| Assembly | |
| Aggregation state | PARTICLE |
|---|---|
| Name | CYTOPLASMIC POLYHEDROSIS VIRUS |
| Virus entity | |
| Virus host category | insect cells |
| Virus host species | Bombyx mori |
| Virus isolate | STRAIN |
| Virus type | virion |
| Buffer | |
| Name | 10MM PBS |
| Experiment | |
| Reconstruction method | SINGLE PARTICLE |
| Specimen type | VITREOUS ICE (CRYO EM) |
| Sample preparation | |
| pH | 7.40 |
| Sample concentration | 3.00 mg/ml |
| Sample support | |
| Details | THE VIRIONS WERE EMBEDDED IN A THIN LAYER OF VITREOUS ICE SUSPENDED ACROSS THE HOLES OF HOLEY CARBON FILMS FOR CRYOEM IMAGING. |
| Vitrification | |
| Details | PLUNGED INTO LIQUID ETHANE |
 Electron Microscopy | |
| Imaging | |
| Microscope | model: FEI POLARA |
|---|---|
| Details | SAMPLES WERE MAINTAINED AT 100K IN THE ELECTRON MICROSCOPE. |
| Electron gun | |
| Electron source | FIELD EMISSION GUN |
| Accelerating voltage | 300 kV |
| Electron dose | 2000.00 e/A**2 |
| Illumination mode | LOW DOSE |
| Lens | |
| Mode | BRIGHT FIELD |
| Magnification | calibrated: 154380 X, nominal: 154380 X |
| Cs | nominal: 2.00 mm |
| Nominal defocus | max: 1300.00 nm, min: 150.00 nm |
| Specimen holder | |
| Temperature | 100.00 Kelvin |
| Detector | |
| Type | TVIPS CCD |
 Processing | |
| 2D projection selection | |
| Number of particles | 12814 |
|---|---|
| Single particle entity | |
| Symmetry type | ICOSAHEDRAL |
| 3D reconstruction | |
| Actual pixel size | 0.972 A/pix |
| CTF correction method | CTF CORRECTION OF EACH PARTICLE |
| Details | PRIOR TO THE MERGING OF PARTICLES FOR 3D RECONSTRUCTION, THE FOURIER TRANSFORM VALUES OF INDIVIDUAL IMAGES WERE CORRECTED FOR THE CTF. |
| Method | FOURIER COMMON LINES AND FOURIER- BESSEL SYNTHESIS |
| Nominal pixel size | 0.972 A/pix |
| Resolution | 3.880 A |
| Refine | |
| Ls d res high | 3.88 A |
| ID | 1 |
| Refine hist | |
| D res high | 3.88 |
| Total atoms | 2199 |
| Protein atoms | 2199 |
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