+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30123 | |||||||||
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Title | Structure of HSV2 viron capsid portal vertex | |||||||||
Map data | ||||||||||
Sample | Human alphaherpesvirus 2 != Human herpesvirus 2 Human alphaherpesvirus 2
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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 | HHV-2 (virus) / Human herpesvirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.39 Å | |||||||||
Authors | Wang XX / 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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30123.map.gz | 151.4 MB | EMDB map data format | |
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Header (meta data) | emd-30123-v30.xml emd-30123.xml | 22.4 KB 22.4 KB | Display Display | EMDB header |
Images | emd_30123.png | 87 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30123 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30123 | HTTPS FTP |
-Validation report
Summary document | emd_30123_validation.pdf.gz | 617.1 KB | Display | EMDB validaton report |
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Full document | emd_30123_full_validation.pdf.gz | 616.6 KB | Display | |
Data in XML | emd_30123_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | emd_30123_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30123 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30123 | HTTPS FTP |
-Related structure data
Related structure data | 6m6gMC 6m6hC 6m6iC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30123.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-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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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-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 |