[English] 日本語
Yorodumi- EMDB-30248: CryoEM structure of VZV A-capsid, 3-fold sub-particle reconstruction -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30248 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CryoEM structure of VZV A-capsid, 3-fold sub-particle reconstruction | |||||||||
Map data | CryoEM structure of VZV A-capsid (3-fold sub-particle reconstruction) | |||||||||
Sample |
| |||||||||
Biological species | Human alphaherpesvirus 3 (Varicella-zoster virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Li S / Zheng Q | |||||||||
Citation | Journal: Nat Microbiol / Year: 2020 Title: Near-atomic cryo-electron microscopy structures of varicella-zoster virus capsids. Authors: Wei Wang / Qingbing Zheng / Dequan Pan / Hai Yu / Wenkun Fu / Jian Liu / Maozhou He / Rui Zhu / Yuze Cai / Yang Huang / Zhenghui Zha / Zhenqin Chen / Xiangzhong Ye / Jinle Han / Yuqiong Que ...Authors: Wei Wang / Qingbing Zheng / Dequan Pan / Hai Yu / Wenkun Fu / Jian Liu / Maozhou He / Rui Zhu / Yuze Cai / Yang Huang / Zhenghui Zha / Zhenqin Chen / Xiangzhong Ye / Jinle Han / Yuqiong Que / Ting Wu / Jun Zhang / Shaowei Li / Hua Zhu / Z Hong Zhou / Tong Cheng / Ningshao Xia / Abstract: Varicella-zoster virus (VZV) is a medically important human herpesvirus that causes chickenpox and shingles, but its cell-associated nature has hindered structure studies. Here we report the cryo- ...Varicella-zoster virus (VZV) is a medically important human herpesvirus that causes chickenpox and shingles, but its cell-associated nature has hindered structure studies. Here we report the cryo-electron microscopy structures of purified VZV A-capsid and C-capsid, as well as of the DNA-containing capsid inside the virion. Atomic models derived from these structures show that, despite enclosing a genome that is substantially smaller than those of other human herpesviruses, VZV has a similarly sized capsid, consisting of 955 major capsid protein (MCP), 900 small capsid protein (SCP), 640 triplex dimer (Tri2) and 320 triplex monomer (Tri1) subunits. The VZV capsid has high thermal stability, although with relatively fewer intra- and inter-capsid protein interactions and less stably associated tegument proteins compared with other human herpesviruses. Analysis with antibodies targeting the N and C termini of the VZV SCP indicates that the hexon-capping SCP-the largest among human herpesviruses-uses its N-terminal half to bridge hexon MCP subunits and possesses a C-terminal flexible half emanating from the inner rim of the upper hexon channel into the tegument layer. Correlation of these structural features and functional observations provide insights into VZV assembly and pathogenesis and should help efforts to engineer gene delivery and anticancer vectors based on the currently available VZV vaccine. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30248.map.gz | 557.3 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-30248-v30.xml emd-30248.xml | 8.6 KB 8.6 KB | Display Display | EMDB header |
Images | emd_30248.png | 207.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30248 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30248 | HTTPS FTP |
-Validation report
Summary document | emd_30248_validation.pdf.gz | 448 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_30248_full_validation.pdf.gz | 447.6 KB | Display | |
Data in XML | emd_30248_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | emd_30248_validation.cif.gz | 9.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30248 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30248 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_30248.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | CryoEM structure of VZV A-capsid (3-fold sub-particle reconstruction) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.307 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Human alphaherpesvirus 3
Entire | Name: Human alphaherpesvirus 3 (Varicella-zoster virus) |
---|---|
Components |
|
-Supramolecule #1: Human alphaherpesvirus 3
Supramolecule | Name: Human alphaherpesvirus 3 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / NCBI-ID: 10335 / Sci species name: Human alphaherpesvirus 3 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
---|
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 56.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 459660 |
---|---|
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |