+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0846 | |||||||||
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Title | Cryo-EM structure of African Swine Fever Virus capsid block 1 | |||||||||
Map data | Cryo-EM structure of African Swine Fever Virus capsid block 1 | |||||||||
Sample |
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Biological species | African swine fever virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.66 Å | |||||||||
Authors | Gao GF / Liu S | |||||||||
Funding support | China, 1 items
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Citation | Journal: Cell Host Microbe / Year: 2019 Title: Cryo-EM Structure of the African Swine Fever Virus. Authors: Sheng Liu / Yuzi Luo / Yajuan Wang / Shihua Li / Zhennan Zhao / Yuhai Bi / Junqing Sun / Ruchao Peng / Hao Song / Dongjie Zhu / Yuan Sun / Su Li / Li Zhang / Wei Wang / Yeping Sun / Jianxun ...Authors: Sheng Liu / Yuzi Luo / Yajuan Wang / Shihua Li / Zhennan Zhao / Yuhai Bi / Junqing Sun / Ruchao Peng / Hao Song / Dongjie Zhu / Yuan Sun / Su Li / Li Zhang / Wei Wang / Yeping Sun / Jianxun Qi / Jinghua Yan / Yi Shi / Xinzheng Zhang / Peiyi Wang / Hua-Ji Qiu / George F Gao / Abstract: African swine fever virus (ASFV) is a large double-stranded DNA virus with an icosahedral multilayered structure. ASFV causes a lethal swine hemorrhagic disease and is currently responsible for ...African swine fever virus (ASFV) is a large double-stranded DNA virus with an icosahedral multilayered structure. ASFV causes a lethal swine hemorrhagic disease and is currently responsible for widespread damage to the pork industry in Asia. Neither vaccines nor antivirals are available and the molecular characterization of the ASFV particle is outstanding. Here, we describe the cryogenic electron microscopy (cryo-EM) structure of the icosahedral capsid of ASFV at 4.6-Å. The ASFV particle consists of 8,280 copies of the major capsid protein p72, 60 copies of the penton protein, and at least 8,340 minor capsid proteins, of which there might be 3 different types. Like other nucleocytoplasmic large DNA viruses, the minor capsid proteins form a hexagonal network below the outer capsid shell, functioning as stabilizers by "gluing" neighboring capsomers together. Our findings provide a comprehensive molecular model of the ASFV capsid architecture that will contribute to the future development of countermeasures, including vaccines. | |||||||||
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_0846.map.gz | 26.4 MB | EMDB map data format | |
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Header (meta data) | emd-0846-v30.xml emd-0846.xml | 10.4 KB 10.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0846_fsc.xml | 15.6 KB | Display | FSC data file |
Images | emd_0846.png | 366.4 KB | ||
Others | emd_0846_additional.map.gz emd_0846_additional_1.map.gz | 163.7 MB 163.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0846 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0846 | HTTPS FTP |
-Validation report
Summary document | emd_0846_validation.pdf.gz | 78.5 KB | Display | EMDB validaton report |
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Full document | emd_0846_full_validation.pdf.gz | 77.6 KB | Display | |
Data in XML | emd_0846_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0846 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0846 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_0846.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of African Swine Fever Virus capsid block 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.41 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Cryo-EM structure of African Swine Fever Virus capsid asymmetric unit
File | emd_0846_additional.map | ||||||||||||
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Annotation | Cryo-EM structure of African Swine Fever Virus capsid asymmetric unit | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Cryo-EM structure of African Swine Fever Virus capsid asymmetric unit
File | emd_0846_additional_1.map | ||||||||||||
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Annotation | Cryo-EM structure of African Swine Fever Virus capsid asymmetric unit | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : African swine fever virus
Entire | Name: African swine fever virus |
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Components |
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-Supramolecule #1: African swine fever virus
Supramolecule | Name: African swine fever virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10497 / Sci species name: African swine fever virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.25 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |