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Yorodumi- EMDB-20558: Atomic Structure of the Human Herpesvirus 6B Capsid and Capsid-As... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20558 | |||||||||||||||
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Title | Atomic Structure of the Human Herpesvirus 6B Capsid and Capsid-Associated Tegument Complexes | |||||||||||||||
Map data | 2-fold sub-particle reconstruction of HHV-6B | |||||||||||||||
Sample |
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Biological species | Human herpesvirus 6 strain Z29 | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.77 Å | |||||||||||||||
Authors | Zhang YB / Liu W / Li ZH / Kumar V / Alvarez-Cabrera AL / Leibovitch E / Cui YX / Mei Y / Bi GQ / Jacobson S / Zhou ZH | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: Nat Commun / Year: 2019 Title: Atomic structure of the human herpesvirus 6B capsid and capsid-associated tegument complexes. Authors: Yibo Zhang / Wei Liu / Zihang Li / Vinay Kumar / Ana L Alvarez-Cabrera / Emily C Leibovitch / Yanxiang Cui / Ye Mei / Guo-Qiang Bi / Steve Jacobson / Z Hong Zhou / Abstract: Human herpesvirus 6B (HHV-6B) belongs to the β-herpesvirus subfamily of the Herpesviridae. To understand capsid assembly and capsid-tegument interactions, here we report atomic structures of HHV-6B ...Human herpesvirus 6B (HHV-6B) belongs to the β-herpesvirus subfamily of the Herpesviridae. To understand capsid assembly and capsid-tegument interactions, here we report atomic structures of HHV-6B capsid and capsid-associated tegument complex (CATC) obtained by cryoEM and sub-particle reconstruction. Compared to other β-herpesviruses, HHV-6B exhibits high similarity in capsid structure but organizational differences in its CATC (pU11 tetramer). 180 "VΛ"-shaped CATCs are observed in HHV-6B, distinguishing from the 255 "Λ"-shaped dimeric CATCs observed in murine cytomegalovirus and the 310 "Δ"-shaped CATCs in human cytomegalovirus. This trend in CATC quantity correlates with the increasing genomes sizes of these β-herpesviruses. Incompatible distances revealed by the atomic structures rationalize the lack of CATC's binding to triplexes Ta, Tc, and Tf in HHV-6B. Our results offer insights into HHV-6B capsid assembly and the roles of its tegument proteins, including not only the β-herpesvirus-specific pU11 and pU14, but also those conserved across all subfamilies of Herpesviridae. | |||||||||||||||
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_20558.map.gz | 413.7 MB | EMDB map data format | |
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Header (meta data) | emd-20558-v30.xml emd-20558.xml | 10.9 KB 10.9 KB | Display Display | EMDB header |
Images | emd_20558.png | 230.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20558 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20558 | HTTPS FTP |
-Validation report
Summary document | emd_20558_validation.pdf.gz | 80 KB | Display | EMDB validaton report |
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Full document | emd_20558_full_validation.pdf.gz | 79.1 KB | Display | |
Data in XML | emd_20558_validation.xml.gz | 496 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20558 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20558 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_20558.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 2-fold sub-particle reconstruction of HHV-6B | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.085 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 herpesvirus 6 strain Z29
Entire | Name: Human herpesvirus 6 strain Z29 |
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Components |
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-Supramolecule #1: Human herpesvirus 6 strain Z29
Supramolecule | Name: Human herpesvirus 6 strain Z29 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 36351 / Sci species name: Human herpesvirus 6 strain Z29 / Sci species strain: Z29 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 / Details: PBS buffer, pH 7.4 |
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Grid | Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: The grids were manually plunged into the ethane.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 23.0 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
Startup model | Type of model: OTHER Details: 3D reconstruction of extracted 2-fold sub-particles |
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Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.77 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 196290 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |
-Atomic model buiding 1
Refinement | Overall B value: 120 |
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