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Open data
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Basic information
Entry | Database: PDB / ID: 5zap | ||||||
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Title | Atomic structure of the herpes simplex virus type 2 B-capsid | ||||||
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![]() | VIRUS / herpesvirus / capsid / cryo-em / atomic structure | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
![]() | Yuan, S. / Wang, J.L. / Zhu, D.J. / Wang, N. / Gao, Q. / Chen, W.Y. / Tang, H. / Wang, J.Z. / Zhang, X.Z. / Liu, H.R. ...Yuan, S. / Wang, J.L. / Zhu, D.J. / Wang, N. / Gao, Q. / Chen, W.Y. / Tang, H. / Wang, J.Z. / Zhang, X.Z. / Liu, H.R. / Rao, Z.H. / Wang, X.X. | ||||||
![]() | ![]() Title: Cryo-EM structure of a herpesvirus capsid at 3.1 Å. Authors: Shuai Yuan / Jialing Wang / Dongjie Zhu / Nan Wang / Qiang Gao / Wenyuan Chen / Hao Tang / Junzhi Wang / Xinzheng Zhang / Hongrong Liu / Zihe Rao / Xiangxi Wang / ![]() Abstract: Structurally and genetically, human herpesviruses are among the largest and most complex of viruses. Using cryo-electron microscopy (cryo-EM) with an optimized image reconstruction strategy, we ...Structurally and genetically, human herpesviruses are among the largest and most complex of viruses. Using cryo-electron microscopy (cryo-EM) with an optimized image reconstruction strategy, we report the herpes simplex virus type 2 (HSV-2) capsid structure at 3.1 angstroms, which is built up of about 3000 proteins organized into three types of hexons (central, peripentonal, and edge), pentons, and triplexes. Both hexons and pentons contain the major capsid protein, VP5; hexons also contain a small capsid protein, VP26; and triplexes comprise VP23 and VP19C. Acting as core organizers, VP5 proteins form extensive intermolecular networks, involving multiple disulfide bonds (about 1500 in total) and noncovalent interactions, with VP26 proteins and triplexes that underpin capsid stability and assembly. Conformational adaptations of these proteins induced by their microenvironments lead to 46 different conformers that assemble into a massive quasisymmetric shell, exemplifying the structural and functional complexity of HSV. #1: ![]() Title: Pushing the resolution limit by correcting the Ewald sphere effect in single-particle Cryo-EM reconstructions. Authors: Dongjie Zhu / Xiangxi Wang / Qianglin Fang / James L Van Etten / Michael G Rossmann / Zihe Rao / Xinzheng Zhang / ![]() ![]() Abstract: The Ewald sphere effect is generally neglected when using the Central Projection Theorem for cryo electron microscopy single-particle reconstructions. This can reduce the resolution of a ...The Ewald sphere effect is generally neglected when using the Central Projection Theorem for cryo electron microscopy single-particle reconstructions. This can reduce the resolution of a reconstruction. Here we estimate the attainable resolution and report a "block-based" reconstruction method for extending the resolution limit. We find the Ewald sphere effect limits the resolution of large objects, especially large viruses. After processing two real datasets of large viruses, we show that our procedure can extend the resolution for both datasets and can accommodate the flexibility associated with large protein complexes. | ||||||
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 4.4 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6907MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 |
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3 | ![]()
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4 | ![]()
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5 | ![]()
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
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Components
#1: Protein | Mass: 149370.359 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 34373.785 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | Mass: 50542.617 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | Mass: 12147.707 Da / Num. of mol.: 15 / 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: Human herpesvirus 2 / Type: VIRUS / Entity ID: #1, #4, #2-#3 / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION |
Natural host | Organism: Human herpesvirus 2 |
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 |
Image recording | Electron dose: 1.1 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
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Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45000 / Symmetry type: POINT |