+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2054 | |||||||||
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Title | Electron cryo-microscopy of Mud Crab Reovirus | |||||||||
Map data | Reconstruction of native Mud Crab Reovirus (MCRV) | |||||||||
Sample |
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Keywords | Mud Crab Reovirus | |||||||||
Biological species | Mud Crab Reovirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 13.8 Å | |||||||||
Authors | Zengwei H / Xiexiong D / Yinyin L / Hongjun S / Kunpeng L / Zhixun G / Peirui Z / Haidong X / Jianguo H / Qinfen Z / Shaoping W | |||||||||
Citation | Journal: Virus Res / Year: 2012 Title: Structural insights into the classification of Mud Crab Reovirus. Authors: Zengwei Huang / Xiexiong Deng / Yinyin Li / Hongjun Su / Kunpeng Li / Zhixun Guo / Peirui Zheng / Haidong Xu / Jianguo He / Qinfen Zhang / Shaoping Weng / Abstract: Cryo-electron microscopy was applied to analyze mud crab reovirus (MCRV), which causes 'sleeping disease' in mud crab, Scylla serrata, a marine species cultured in China. We present here the three ...Cryo-electron microscopy was applied to analyze mud crab reovirus (MCRV), which causes 'sleeping disease' in mud crab, Scylla serrata, a marine species cultured in China. We present here the three dimensional structure of MCRV at 13.8Å resolution. The outer capsid shell is composed of 260 trimers with complete T=13 icosahedral symmetry. A major difference between MCRV and previously reported aquareoviruses is that it lacks a pentameric turret structure. These results together with recently published molecular biological evidence (Deng et al., 2012) indicate that, from a structural perspective, MCRV should be classified as a new member of the family Reoviridae. | |||||||||
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_2054.map.gz | 31.2 MB | EMDB map data format | |
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Header (meta data) | emd-2054-v30.xml emd-2054.xml | 9.3 KB 9.3 KB | Display Display | EMDB header |
Images | image2054.png | 530.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2054 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2054 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2054.map.gz / Format: CCP4 / Size: 36.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of native Mud Crab Reovirus (MCRV) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.7 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 : Mud Crab Reovirus (MCRV)
Entire | Name: Mud Crab Reovirus (MCRV) |
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Components |
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-Supramolecule #1000: Mud Crab Reovirus (MCRV)
Supramolecule | Name: Mud Crab Reovirus (MCRV) / type: sample / ID: 1000 / Oligomeric state: icosahedral / Number unique components: 1 |
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-Supramolecule #1: Mud Crab Reovirus
Supramolecule | Name: Mud Crab Reovirus / type: virus / ID: 1 / Name.synonym: Mud Crab Reovirus / Sci species name: Mud Crab Reovirus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No / Syn species name: Mud Crab Reovirus |
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Host (natural) | Organism: Scylla serrata (giant mud crab) / synonym: INVERTEBRATES |
Virus shell | Shell ID: 1 / Diameter: 724 Å / T number (triangulation number): 13 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 / Details: 0.1M PBS |
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Grid | Details: R1.2/1.3 Quantifoil grids(200mesh) with thin carbon film |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: freezed by manual / Method: blot about 5 seconds by manual before plunging |
-Electron microscopy
Microscope | JEOL 2010 |
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Electron beam | Acceleration voltage: 200 kV / Electron source: LAB6 |
Electron optics | Calibrated magnification: 46900 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Liquid nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN |
Temperature | Min: 100 K / Max: 103 K / Average: 102 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 400,000 times magnification |
Details | Miminum dose illumination (MDS model) |
Date | Jan 12, 2009 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON COOLSCAN / Digitization - Sampling interval: 6.5 µm / Number real images: 100 / Average electron dose: 18 e/Å2 / Bits/pixel: 16 |
-Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 13.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 4020 |
Details | The particles were selected by EMAN boxer programms. |