|Entry||Database: PDB / ID: 3cnf|
|Title||3.88 Angstrom structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy|
|Keywords||VIRUS / cytoplasmic polyhedrosis virus / capsid protein / turret protein / polyhedrin-binding domain / guanylyltransferase domain / icosahedral virus|
|Specimen source||Bombyx mori cypovirus 1 / virus / image: Bombyx mori|
|Method||Electron microscopy (3.88 Å resolution / Particle / Single particle)|
|Authors||Yu, X. / Jin, L. / Zhou, Z.H.|
|Citation||Nature, 2008, 453, 415-419|
SummaryFull reportAbout validation report
|Date||Deposition: Mar 25, 2008 / Release: Apr 29, 2008|
Downloads & links
A: VP1x 60
A: VP1x 5
A: VP1x 6
Mass: 148560.859 Da / Num. of mol.: 2
Source: (natural) Bombyx mori cypovirus 1 / virus / image: Bombyx mori
References: UniProt: Q6TS43
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE|
|Component||Name: CYTOPLASMIC POLYHEDROSIS VIRUS / Type: VIRUS|
|Details of virus||Virus host category: INSECT / Virus isolate: STRAIN / Virus type: VIRION|
|Natural host||Organism: Bombyx mori|
|Buffer solution||Name: 10MM PBS / Details: 10MM PBS / pH: 7.4|
|Specimen||Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen 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||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: PLUNGED INTO LIQUID ETHANE|
-Electron microscopy imaging
Model: Tecnai Polara / Image courtesy: FEI Company
|Microscopy||Microscope model: FEI POLARA 300|
Details: SAMPLES WERE MAINTAINED AT 100K IN THE ELECTRON MICROSCOPE.
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELD / Nominal magnification: 154380 / Calibrated magnification: 154380 / Nominal defocus max: 13 nm / Nominal defocus min: 15 nm / Cs: 2 mm|
|Specimen holder||Temperature: 1 kelvins|
|Image recording||Electron dose: 20 e/Å2 / Film or detector model: GENERIC TVIPS|
|Radiation||Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray|
|Radiation wavelength||Relative weight: 1|
|CTF correction||Details: CTF CORRECTION OF EACH PARTICLE|
|Symmetry||Point symmetry: I|
|3D reconstruction||Method: FOURIER COMMON LINES AND FOURIER- BESSEL SYNTHESIS / Resolution: 3.88 Å / Number of particles: 12814 / Nominal pixel size: 0.972 / Actual pixel size: 0.972|
Details: PRIOR TO THE MERGING OF PARTICLES FOR 3D RECONSTRUCTION, THE FOURIER TRANSFORM VALUES OF INDIVIDUAL IMAGES WERE CORRECTED FOR THE CTF.
Symmetry type: POINT
|Least-squares process||Highest resolution: 3.88 Å|
|Refine hist #LAST||Highest resolution: 3.88 Å|
|Number of atoms included #LAST||Protein: 2199 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 2199|
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