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Yorodumi- EMDB-1508: 3.88 Angstrom structure of cytoplasmic polyhedrosis virus by sing... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1508 | |||||||||
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Title | 3.88 Angstrom structure of cytoplasmic polyhedrosis virus by single-particle cryo-electron microscopy | |||||||||
Map data | This is the whole cryoEM 2f map for the icosahedral Cytoplasmic Polyhedrosis Virus (CPV). | |||||||||
Sample |
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Keywords | virus / strcuture / CPV / cryo-electron microscopy | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Bombyx mori cypovirus 1 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.88 Å | |||||||||
Authors | YU X / Jin L / Zhou ZH | |||||||||
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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1508.map.gz | 187.6 MB | EMDB map data format | |
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Header (meta data) | emd-1508-v30.xml emd-1508.xml | 11.2 KB 11.2 KB | Display Display | EMDB header |
Images | 1508.gif | 103.8 KB | ||
Masks | emd_1508_msk_1.map | 14.9 MB | Mask map | |
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1508 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1508 | HTTPS FTP |
-Validation report
Summary document | emd_1508_validation.pdf.gz | 414 KB | Display | EMDB validaton report |
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Full document | emd_1508_full_validation.pdf.gz | 413.6 KB | Display | |
Data in XML | emd_1508_validation.xml.gz | 9.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1508 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1508 | HTTPS FTP |
-Related structure data
Related structure data | 3cnfMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_1508.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is the whole cryoEM 2f map for the icosahedral Cytoplasmic Polyhedrosis Virus (CPV). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.97 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Segmentation: This is a segment of the asymmetric unit
Annotation | This is a segment of the asymmetric unit | ||||||||||||
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File | emd_1508_msk_1.map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : cytoplasmic polyhedrosis virus
Entire | Name: cytoplasmic polyhedrosis virus |
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Components |
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-Supramolecule #1000: cytoplasmic polyhedrosis virus
Supramolecule | Name: cytoplasmic polyhedrosis virus / type: sample / ID: 1000 / Details: whole infectious virus / Oligomeric state: icosahedral particle of whole virus / Number unique components: 5 |
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-Supramolecule #1: Bombyx mori cypovirus 1
Supramolecule | Name: Bombyx mori cypovirus 1 / type: virus / ID: 1 / Name.synonym: CPV Details: CPV is an unenveloped virus wiht a single-shell capsid and diameter of 750 Angstroms. NCBI-ID: 110829 / Sci species name: Bombyx mori cypovirus 1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: CPV |
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Host (natural) | Organism: Bombyx mori (domestic silkworm) / synonym: INVERTEBRATES |
Virus shell | Shell ID: 1 / Diameter: 750 Å / T number (triangulation number): 1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 / Details: 10mM PBS |
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Grid | Details: the holes of holey carbon films |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 100 K / Instrument: HOMEMADE PLUNGER Details: Vitrification instrument: lab-made plunger. Vitrification was carried out at room temperature. CPV were embedded in a thin layer of vitreous ice suspended across the holes of holey carbon ...Details: Vitrification instrument: lab-made plunger. Vitrification was carried out at room temperature. CPV were embedded in a thin layer of vitreous ice suspended across the holes of holey carbon films for cryoEM imaging. Method: blot for 3 seconds wiht filter paper before plunging |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Average: 100 K |
Image recording | Category: CCD / Film or detector model: GENERIC TVIPS / Average electron dose: 20 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 154380 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 1.3 µm / Nominal defocus min: 0.15 µm / Nominal magnification: 154380 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Details | Focal pairs of micrographs were recorded on 4KX4K charge-coupled device (CCD) camera. |
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CTF correction | Details: each particle |
Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.88 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMIRS Details: Determination of particle orientation and center parameters and subsequent 3D reconstruction were carried out using programs in the IMIRS software package, which are based on Fourier common ...Details: Determination of particle orientation and center parameters and subsequent 3D reconstruction were carried out using programs in the IMIRS software package, which are based on Fourier common lines and Fourier-Bessel synthesis methods. Prior to the merging of particles for 3D reconstruction, the Fourier transform values of individual images were corrected for the CTF with 15 percent amplitude contrast and a decay factor of 35 sq. Angstroms. Number images used: 12814 |