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Open data
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Basic information
Entry | Database: PDB / ID: 8hif | ||||||
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Title | One asymmetric unit of Singapore grouper iridovirus capsid | ||||||
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![]() | VIRAL PROTEIN / Singapore grouper iridovirus / capsid proteins | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
![]() | Zhao, Z.N. / Liu, C.C. / Zhu, D.J. / Qi, J.X. / Zhang, X.Z. / Gao, G.F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Near-atomic architecture of Singapore grouper iridovirus and implications for giant virus assembly. Authors: Zhennan Zhao / Youhua Huang / Congcong Liu / Dongjie Zhu / Shuaixin Gao / Sheng Liu / Ruchao Peng / Ya Zhang / Xiaohong Huang / Jianxun Qi / Catherine C L Wong / Xinzheng Zhang / Peiyi Wang ...Authors: Zhennan Zhao / Youhua Huang / Congcong Liu / Dongjie Zhu / Shuaixin Gao / Sheng Liu / Ruchao Peng / Ya Zhang / Xiaohong Huang / Jianxun Qi / Catherine C L Wong / Xinzheng Zhang / Peiyi Wang / Qiwei Qin / George F Gao / ![]() ![]() Abstract: Singapore grouper iridovirus (SGIV), one of the nucleocytoviricota viruses (NCVs), is a highly pathogenic iridovirid. SGIV infection results in massive economic losses to the aquaculture industry and ...Singapore grouper iridovirus (SGIV), one of the nucleocytoviricota viruses (NCVs), is a highly pathogenic iridovirid. SGIV infection results in massive economic losses to the aquaculture industry and significantly threatens global biodiversity. In recent years, high morbidity and mortality in aquatic animals have been caused by iridovirid infections worldwide. Effective control and prevention strategies are urgently needed. Here, we present a near-atomic architecture of the SGIV capsid and identify eight types of capsid proteins. The viral inner membrane-integrated anchor protein colocalizes with the endoplasmic reticulum (ER), supporting the hypothesis that the biogenesis of the inner membrane is associated with the ER. Additionally, immunofluorescence assays indicate minor capsid proteins (mCPs) could form various building blocks with major capsid proteins (MCPs) before the formation of a viral factory (VF). These results expand our understanding of the capsid assembly of NCVs and provide more targets for vaccine and drug design to fight iridovirid infections. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 9.4 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 1.1 MB | Display | |
Data in CIF | ![]() | 1.8 MB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 34815MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 7 types, 144 molecules A1A2A3B1B2B3C1C2C3D1D2D3E1E2E3F1F2F3G1G2G3H1H2H3I1I2I3J1J3K1...
#1: Protein | Mass: 50573.141 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 19070.715 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | Mass: 49777.852 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Protein | | Mass: 54052.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #5: Protein | | Mass: 16343.806 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #6: Protein | | Mass: 11354.337 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #7: Protein | | Mass: 15872.862 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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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 |
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Sample preparation
Component | Name: Singapore grouper iridovirus / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1300 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
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Processing
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37161 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 82.32 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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