+Open data
-Basic information
Entry | Database: PDB / ID: 7bw6 | ||||||
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Title | Varicella-zoster virus capsid | ||||||
Components |
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Keywords | VIRUS / A-capsid | ||||||
Function / homology | Function and homology information T=16 icosahedral viral capsid / viral capsid assembly / viral process / viral capsid / host cell nucleus / structural molecule activity / DNA binding Similarity search - Function | ||||||
Biological species | Human herpesvirus 3 (Varicella-zoster virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
Authors | Wang, P.Y. / Qi, J.X. / Liu, C.C. / Sun, J.Q. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2020 Title: Cryo-EM structure of the varicella-zoster virus A-capsid. Authors: Junqing Sun / Congcong Liu / Ruchao Peng / Fu-Kun Zhang / Zhou Tong / Sheng Liu / Yi Shi / Zhennan Zhao / Wen-Bo Zeng / George Fu Gao / Hong-Jie Shen / Xiaoming Yang / Minhua Luo / Jianxun Qi / Peiyi Wang / Abstract: Varicella-zoster virus (VZV), a member of the Alphaherpesvirinae subfamily, causes severe diseases in humans of all ages. The viral capsids play critical roles in herpesvirus infection, making them ...Varicella-zoster virus (VZV), a member of the Alphaherpesvirinae subfamily, causes severe diseases in humans of all ages. The viral capsids play critical roles in herpesvirus infection, making them potential antiviral targets. Here, we present the 3.7-Å-resolution structure of the VZV A-capsid and define the molecular determinants underpinning the assembly of this complicated viral machinery. Overall, the VZV capsid has a similar architecture to that of other known herpesviruses. The major capsid protein (MCP) assembles into pentons and hexons, forming extensive intra- and inter-capsomer interaction networks that are further secured by the small capsid protein (SCP) and the heterotriplex. The structure reveals a pocket beneath the floor of MCP that could potentially be targeted by antiviral inhibitors. In addition, we identified two alphaherpesvirus-specific structural features in SCP and Tri1 proteins. These observations highlight the divergence of different herpesviruses and provide an important basis for developing antiviral drugs. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7bw6.cif.gz | 4.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7bw6.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7bw6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bw6_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7bw6_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7bw6_validation.xml.gz | 551.1 KB | Display | |
Data in CIF | 7bw6_validation.cif.gz | 899.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/7bw6 ftp://data.pdbj.org/pub/pdb/validation_reports/bw/7bw6 | HTTPS FTP |
-Related structure data
Related structure data | 30228MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 155145.359 Da / Num. of mol.: 16 / Source method: isolated from a natural source Source: (natural) Human herpesvirus 3 (Varicella-zoster virus) References: UniProt: Q6QCL5 #2: Protein | Mass: 24440.119 Da / Num. of mol.: 15 / Source method: isolated from a natural source Source: (natural) Human herpesvirus 3 (Varicella-zoster virus) References: UniProt: Q6QCN2 #3: Protein | Mass: 34421.914 Da / Num. of mol.: 10 / Source method: isolated from a natural source Source: (natural) Human herpesvirus 3 (Varicella-zoster virus) References: UniProt: Q6QCL4 #4: Protein | Mass: 54028.180 Da / Num. of mol.: 5 / Source method: isolated from a natural source Source: (natural) Human herpesvirus 3 (Varicella-zoster virus) References: UniProt: Q6QCN5 |
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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 |
-Sample preparation
Component | Name: Human alphaherpesvirus 3 / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Human alphaherpesvirus 3 (Varicella-zoster virus) |
Details of virus | Empty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Homemade |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blot for 2 seconds before plunging |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 59000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 386.3 nm / Calibrated defocus max: 5116 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: BASIC |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 93 K / Temperature (min): 81 K |
Image recording | Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 26979 |
Image scans | Width: 4096 / Height: 4096 |
-Processing
Software |
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 94640 Details: Images were low-pass to 15 angstrom to facilitated particle picking. | ||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 311236 / Num. of class averages: 5 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 101.55 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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