+Open data
-Basic information
Entry | Database: PDB / ID: 6m6g | ||||||
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Title | Structure of HSV2 viron 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: 5.39 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 | 6m6g.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6m6g.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 6m6g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6m6g_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6m6g_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6m6g_validation.xml.gz | 254.8 KB | Display | |
Data in CIF | 6m6g_validation.cif.gz | 390 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m6/6m6g ftp://data.pdbj.org/pub/pdb/validation_reports/m6/6m6g | HTTPS FTP |
-Related structure data
Related structure data | 30123MC 6m6hC 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 , 5 types, 16 molecules BCDEFIGMQTUVLPno
#1: Protein | Mass: 149398.422 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 2 / References: UniProt: P89442 #2: Protein | Mass: 12117.615 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 2 / References: UniProt: G9I257 #4: Protein | | Mass: 7166.825 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 2 #5: Protein | | Mass: 7422.140 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 2 #9: Protein | Mass: 330425.906 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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-Triplex capsid protein ... , 2 types, 3 molecules KOS
#3: Protein | Mass: 34373.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 2 / References: UniProt: G9I239 #6: Protein | | Mass: 50566.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 2 / References: UniProt: G9I260 |
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-Capsid vertex component ... , 2 types, 3 molecules klm
#7: Protein | Mass: 74793.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 2 / References: UniProt: P89440 |
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#8: Protein | Mass: 63637.820 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 2 / References: UniProt: P89448 |
-Details
Sequence details | Sequence for Coiled coils chains could not be identified. |
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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 herpesvirus 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: 5.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12001 / Symmetry type: POINT |