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Yorodumi- EMDB-6468: Uncoating Mechanism of Carnation Mottle Virus Revealed by Cryo-EM... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6468 | |||||||||
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Title | Uncoating Mechanism of Carnation Mottle Virus Revealed by Cryo-EM Single Particle Analysis | |||||||||
Map data | Ca-pH7 | |||||||||
Sample |
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Biological species | Carnation mottle virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.4 Å | |||||||||
Authors | Wang CY / Zhang QF / Gao YZ / Xie L / Li HM / Hong J / Zhang CX | |||||||||
Citation | Journal: Sci Rep / Year: 2015 Title: Uncoating Mechanism of Carnation Mottle Virus Revealed by Cryo-EM Single Particle Analysis. Authors: Chun-Yan Wang / Qin-Fen Zhang / Yuan-Zhu Gao / Li Xie / Hong-Mei Li / Jian Hong / Chuan-Xi Zhang / Abstract: Genome uncoating is a prerequisite for the successful infection of plant viruses in host plants. Thus far, little is known about the genome uncoating of the Carnation mottle virus (CarMV). Here, we ...Genome uncoating is a prerequisite for the successful infection of plant viruses in host plants. Thus far, little is known about the genome uncoating of the Carnation mottle virus (CarMV). Here, we obtained two reconstructions of CarMV at pH7 in the presence (Ca-pH7) and absence (EDTA-pH7) of calcium ions by Cryo-EM single particle analysis, which achieved 6.4 Å and 8 Å resolutions respectively. Our results showed that chelation of the calcium ions under EDTA-pH7 resulted in reduced interaction between the subunits near the center of the asymmetric unit but not overall size change of the viral particles, which indicated that the role of the calcium ions in CarMV was not predominantly for the structural preservation. Part of the genomic RNA closest to the capsid was found to be located near the center of the asymmetric unit, which might result from the interaction between genomic RNA and Lys194 residues. Together with the electrostatic potential analysis on the inner surface of the asymmetric unit, the reduced interaction near the center of the asymmetric unit under EDTA-pH7 suggested that the genome release of CarMV might be realized through the center of the asymmetric unit. | |||||||||
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_6468.map.gz | 156.1 MB | EMDB map data format | |
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Header (meta data) | emd-6468-v30.xml emd-6468.xml | 7.3 KB 7.3 KB | Display Display | EMDB header |
Images | 400_6468.gif 80_6468.gif | 143.2 KB 24.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6468 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6468 | HTTPS FTP |
-Validation report
Summary document | emd_6468_validation.pdf.gz | 79.7 KB | Display | EMDB validaton report |
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Full document | emd_6468_full_validation.pdf.gz | 78.8 KB | Display | |
Data in XML | emd_6468_validation.xml.gz | 495 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6468 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6468 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6468.map.gz / Format: CCP4 / Size: 268.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Ca-pH7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.192 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Carnation mottle virus
Entire | Name: Carnation mottle virus |
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Components |
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-Supramolecule #1000: Carnation mottle virus
Supramolecule | Name: Carnation mottle virus / type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: Carnation mottle virus
Supramolecule | Name: Carnation mottle virus / type: virus / ID: 1 / NCBI-ID: 11986 / Sci species name: Carnation mottle virus / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Dianthus caryophyllus (clove pink) / synonym: PLANTAE(HIGHER PLANTS) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: NITROGEN / Instrument: FEI VITROBOT MARK II |
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-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | Oct 11, 2012 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 6.4 Å / Resolution method: OTHER / Number images used: 8400 |
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-Atomic model buiding 1
Initial model | PDB ID: |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT |