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Yorodumi- PDB-3cnf: 3.88 Angstrom structure of cytoplasmic polyhedrosis virus by cryo... -
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-Basic information
Entry | Database: PDB / ID: 3cnf | ||||||
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Title | 3.88 Angstrom structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy | ||||||
Components |
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Keywords | VIRUS / cytoplasmic polyhedrosis virus / capsid protein / turret protein / polyhedrin-binding domain / guanylyltransferase domain / icosahedral virus | ||||||
Function / homology | : / : / CPV Capsid shell protein VP1, small protrusion domain / Inner layer core protein VP1-like, C-terminal / T=2 icosahedral viral capsid / viral inner capsid / Capsid protein VP1 / VP3 Function and homology information | ||||||
Biological species | Bombyx mori cypovirus 1 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.88 Å | ||||||
Authors | Yu, X. / Jin, L. / Zhou, Z.H. | ||||||
Citation | Journal: Nature / Year: 2008 Title: 3.88 A structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy. Authors: Xuekui Yu / Lei Jin / Z Hong Zhou / Abstract: Cytoplasmic polyhedrosis virus (CPV) is unique within the Reoviridae family in having a turreted single-layer capsid contained within polyhedrin inclusion bodies, yet being fully capable of cell ...Cytoplasmic polyhedrosis virus (CPV) is unique within the Reoviridae family in having a turreted single-layer capsid contained within polyhedrin inclusion bodies, yet being fully capable of cell entry and endogenous RNA transcription. Biochemical data have shown that the amino-terminal 79 residues of the CPV turret protein (TP) is sufficient to bring CPV or engineered proteins into the polyhedrin matrix for micro-encapsulation. Here we report the three-dimensional structure of CPV at 3.88 A resolution using single-particle cryo-electron microscopy. Our map clearly shows the turns and deep grooves of alpha-helices, the strand separation in beta-sheets, and densities for loops and many bulky side chains; thus permitting atomic model-building effort from cryo-electron microscopy maps. We observed a helix-to-beta-hairpin conformational change between the two conformational states of the capsid shell protein in the region directly interacting with genomic RNA. We have also discovered a messenger RNA release hole coupled with the mRNA capping machinery unique to CPV. Furthermore, we have identified the polyhedrin-binding domain, a structure that has potential in nanobiotechnology applications. | ||||||
History |
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-Structure visualization
Movie |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3cnf.cif.gz | 112.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cnf.ent.gz | 52.4 KB | Display | PDB format |
PDBx/mmJSON format | 3cnf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cnf_validation.pdf.gz | 1005.3 KB | Display | wwPDB validaton report |
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Full document | 3cnf_full_validation.pdf.gz | 1006.7 KB | Display | |
Data in XML | 3cnf_validation.xml.gz | 33.8 KB | Display | |
Data in CIF | 3cnf_validation.cif.gz | 49.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/3cnf ftp://data.pdbj.org/pub/pdb/validation_reports/cn/3cnf | HTTPS FTP |
-Related structure data
Related structure data | 1508MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 148560.859 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bombyx mori cypovirus 1 / References: UniProt: Q6TS43 #2: Protein | | Mass: 119747.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: The cytoplasmic polyhedrosis virus was isolated and purified from infected Bombyx mori larvae. Source: (natural) Bombyx mori cypovirus 1 / References: UniProt: Q9E957 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: CYTOPLASMIC POLYHEDROSIS VIRUS / Type: VIRUS |
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Details of virus | Host category: INSECT / Isolate: STRAIN / Type: VIRION |
Natural host | Organism: Bombyx mori |
Buffer solution | Name: 10MM PBS / pH: 7.4 / Details: 10MM PBS |
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
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | 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 X / Calibrated magnification: 154380 X / Nominal defocus max: 1300 nm / Nominal defocus min: 150 nm / Cs: 2 mm |
Specimen holder | Temperature: 100 K |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: GENERIC TVIPS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
CTF correction | Details: CTF CORRECTION OF EACH PARTICLE | ||||||||||||
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Symmetry | Point symmetry: I (icosahedral) | ||||||||||||
3D reconstruction | Method: FOURIER COMMON LINES AND FOURIER- BESSEL SYNTHESIS / Resolution: 3.88 Å / Num. of particles: 12814 / Nominal pixel size: 0.972 Å / Actual pixel size: 0.972 Å 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 | ||||||||||||
Refinement | Highest resolution: 3.88 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 3.88 Å
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