+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30122 | |||||||||
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Title | Asymmetric reconstrcution of HSV2 C capsid | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Human alphaherpesvirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.0 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_30122.map.gz | 220.8 MB | EMDB map data format | |
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Header (meta data) | emd-30122-v30.xml emd-30122.xml | 7.8 KB 7.8 KB | Display Display | EMDB header |
Images | emd_30122.png | 84.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30122 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30122 | HTTPS FTP |
-Validation report
Summary document | emd_30122_validation.pdf.gz | 426.4 KB | Display | EMDB validaton report |
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Full document | emd_30122_full_validation.pdf.gz | 426 KB | Display | |
Data in XML | emd_30122_validation.xml.gz | 8.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30122 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30122 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_30122.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 2.76 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
Entire | Name: Human alphaherpesvirus 2 |
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Components |
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-Supramolecule #1: Human alphaherpesvirus 2
Supramolecule | Name: Human alphaherpesvirus 2 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10310 / Sci species name: Human alphaherpesvirus 2 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No |
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Host (natural) | Organism: Homo sapiens (human) |
-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 | Film or detector model: FEI FALCON II (4k x 4k) / 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
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 71956 |
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Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |