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Yorodumi- EMDB-21505: Structures of Capsid and Capsid-Associated Tegument Complex insid... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21505 | |||||||||||||||
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Title | Structures of Capsid and Capsid-Associated Tegument Complex inside the Epstein-Barr Virus | |||||||||||||||
Map data | C5 reconstruction of a portal-containing EBV capsid | |||||||||||||||
Sample |
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Biological species | Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8)) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.8 Å | |||||||||||||||
Authors | Liu W / Cui YX / Wang CY / Li ZH / Gong DY / Dai XH / Bi GQ / Sun R / Zhou ZH | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: Nat Microbiol / Year: 2020 Title: Structures of capsid and capsid-associated tegument complex inside the Epstein-Barr virus. Authors: Wei Liu / Yanxiang Cui / Caiyan Wang / Zihang Li / Danyang Gong / Xinghong Dai / Guo-Qiang Bi / Ren Sun / Z Hong Zhou / Abstract: As the first discovered human cancer virus, Epstein-Barr virus (EBV) causes Burkitt's lymphoma and nasopharyngeal carcinoma. Isolating virions for determining high-resolution structures has been ...As the first discovered human cancer virus, Epstein-Barr virus (EBV) causes Burkitt's lymphoma and nasopharyngeal carcinoma. Isolating virions for determining high-resolution structures has been hindered by latency-a hallmark of EBV infection-and atomic structures are thus available only for recombinantly expressed EBV proteins. In the present study, by symmetry relaxation and subparticle reconstruction, we have determined near-atomic-resolution structures of the EBV capsid with an asymmetrically attached DNA-translocating portal and capsid-associated tegument complexes from cryogenic electron microscopy images of just 2,048 EBV virions obtained by chemical induction. The resulting atomic models reveal structural plasticity among the 20 conformers of the major capsid protein, 2 conformers of the small capsid protein (SCP), 4 conformers of the triplex monomer proteins and 2 conformers of the triplex dimer proteins. Plasticity reaches the greatest level at the capsid-tegument interfaces involving SCP and capsid-associated tegument complexes (CATC): SCPs crown pentons/hexons and mediate tegument protein binding, and CATCs bind and rotate all five periportal triplexes, but notably only about one peri-penton triplex. These results offer insights into the EBV capsid assembly and a mechanism for recruiting cell-regulating factors into the tegument compartment as 'cargoes', and should inform future anti-EBV strategies. | |||||||||||||||
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_21505.map.gz | 460.2 MB | EMDB map data format | |
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Header (meta data) | emd-21505-v30.xml emd-21505.xml | 12.7 KB 12.7 KB | Display Display | EMDB header |
Images | emd_21505.png | 127.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21505 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21505 | HTTPS FTP |
-Validation report
Summary document | emd_21505_validation.pdf.gz | 79.5 KB | Display | EMDB validaton report |
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Full document | emd_21505_full_validation.pdf.gz | 78.6 KB | Display | |
Data in XML | emd_21505_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21505 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21505 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_21505.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | C5 reconstruction of a portal-containing EBV capsid | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.72 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 4 strain B95-8
Entire | Name: Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8)) |
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Components |
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-Supramolecule #1: Human herpesvirus 4 strain B95-8
Supramolecule | Name: Human herpesvirus 4 strain B95-8 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10377 / Sci species name: Human herpesvirus 4 strain B95-8 / 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 | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa |
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) / Number real images: 1833 / Average electron dose: 28.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 4.0 µm / Calibrated defocus min: 0.8 µm / Calibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER / Details: 3D reconstruction of portal-containing particles |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 7.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1959 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |