+Open data
-Basic information
Entry | Database: PDB / ID: 6m6h | ||||||
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Title | Structure of HSV2 C-capsid portal vertex | ||||||
Components |
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Keywords | VIRAL PROTEIN / HSV2 / Portal vertex / Complex | ||||||
Function / homology | Function and homology information T=16 icosahedral viral capsid / deNEDDylase activity / viral genome packaging / viral tegument / viral capsid assembly / viral DNA genome replication / chromosome organization / viral process / virion component / viral penetration into host nucleus ...T=16 icosahedral viral capsid / deNEDDylase activity / viral genome packaging / viral tegument / viral capsid assembly / viral DNA genome replication / chromosome organization / viral process / virion component / viral penetration into host nucleus / host cell / viral capsid / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / host cell cytoplasm / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / symbiont entry into host cell / host cell nucleus / structural molecule activity / proteolysis / DNA binding Similarity search - Function | ||||||
Biological species | Human herpesvirus 2 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å | ||||||
Authors | Wang, X.X. / Wang, N. | ||||||
Citation | Journal: Protein Cell / Year: 2020 Title: Structures of the portal vertex reveal essential protein-protein interactions for Herpesvirus assembly and maturation. Authors: Nan Wang / Wenyuan Chen / Ling Zhu / Dongjie Zhu / Rui Feng / Jialing Wang / Bin Zhu / Xinzheng Zhang / Xiaoqing Chen / Xianjie Liu / Runbin Yan / Dongyao Ni / Grace Guoying Zhou / Hongrong ...Authors: Nan Wang / Wenyuan Chen / Ling Zhu / Dongjie Zhu / Rui Feng / Jialing Wang / Bin Zhu / Xinzheng Zhang / Xiaoqing Chen / Xianjie Liu / Runbin Yan / Dongyao Ni / Grace Guoying Zhou / Hongrong Liu / Zihe Rao / Xiangxi Wang / | ||||||
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 | 6m6h.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6m6h.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 6m6h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6m6h_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6m6h_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6m6h_validation.xml.gz | 253 KB | Display | |
Data in CIF | 6m6h_validation.cif.gz | 389.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m6/6m6h ftp://data.pdbj.org/pub/pdb/validation_reports/m6/6m6h | HTTPS FTP |
-Related structure data
Related structure data | 30124MC 6m6gC 6m6iC 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: C5 (5 fold cyclic)) |
-Components
-Protein , 3 types, 14 molecules ABCDEFJKLMNOPQ
#1: Protein | Mass: 149399.359 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 2 / References: UniProt: P89442 #4: Protein | Mass: 12147.707 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 2 / References: UniProt: G9I257 #5: Protein | Mass: 330496.031 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 2 References: UniProt: P89459, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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-Capsid vertex component ... , 2 types, 3 molecules GHI
#2: Protein | Mass: 74811.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 2 / References: UniProt: P89440 |
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#3: Protein | Mass: 63604.750 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 2 / References: UniProt: P89448 |
-Triplex capsid protein ... , 2 types, 3 molecules RST
#6: Protein | Mass: 34373.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 2 / References: UniProt: G9I239 #7: Protein | | Mass: 50512.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 2 / References: UniProt: G9I260 |
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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 2 / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Human alphaherpesvirus 2 |
Details of virus | Empty: NO / Enveloped: YES / Isolate: SPECIES / Type: VIRION |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: DARK FIELD | ||||||||||||
Image recording |
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-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35698 / Symmetry type: POINT |