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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-30123 | |||||||||
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Title | Structure of HSV2 viron capsid portal vertex | |||||||||
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![]() | Human alphaherpesvirus 2 != Human herpesvirus 2 Human alphaherpesvirus 2
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Function / homology | ![]() T=16 icosahedral viral capsid / deNEDDylase activity / viral genome packaging / viral tegument / viral capsid assembly / viral DNA genome replication / viral release from host cell / chromosome organization / viral process / viral penetration into host nucleus ...T=16 icosahedral viral capsid / deNEDDylase activity / viral genome packaging / viral tegument / viral capsid assembly / viral DNA genome replication / viral release from host cell / chromosome organization / viral process / viral penetration into host nucleus / 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 | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.39 Å | |||||||||
![]() | Wang XX / Wang N | |||||||||
![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 151.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 22.4 KB 22.4 KB | Display Display | ![]() |
Images | ![]() | 87 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 617.1 KB | Display | ![]() |
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Full document | ![]() | 616.6 KB | Display | |
Data in XML | ![]() | 6.6 KB | Display | |
Data in CIF | ![]() | 7.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6m6gMC ![]() 6m6hC ![]() 6m6iC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : Human alphaherpesvirus 2
+Supramolecule #1: Human herpesvirus 2
+Macromolecule #1: Major capsid protein
+Macromolecule #2: Small capsomere-interacting protein
+Macromolecule #3: Triplex capsid protein 2
+Macromolecule #4: coiled coils
+Macromolecule #5: Coiled coils
+Macromolecule #6: Triplex capsid protein 1
+Macromolecule #7: Capsid vertex component 1
+Macromolecule #8: Capsid vertex component 2
+Macromolecule #9: Large tegument protein deneddylase
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | #0 - Image recording ID: 1 / #0 - Film or detector model: FEI FALCON II (4k x 4k) / #0 - Average electron dose: 30.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: FEI FALCON II (4k x 4k) / #1 - Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Image recording ID | 1 |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 5.39 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12001 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |