+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17414 | |||||||||
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Title | Cryo-electron tomogram of isolated Vaccinia Virus cores | |||||||||
Map data | IsoNet corrected cryo-electron tomogram of isolated Vaccinia Virus cores | |||||||||
Sample |
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Keywords | Poxvirus / Vaccinia Virus / core / cryo-electron tomography / AlphaFold / VIRAL PROTEIN | |||||||||
Biological species | Vaccinia virus Western Reserve | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Datler J / Hansen JM / Thader A / Schloegl A / Hodirnau VV / Schur FKM | |||||||||
Funding support | 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 Title: Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Authors: Julia Datler / Jesse M Hansen / Andreas Thader / Alois Schlögl / Lukas W Bauer / Victor-Valentin Hodirnau / Florian K M Schur / Abstract: Poxviruses are among the largest double-stranded DNA viruses, with members such as variola virus, monkeypox virus and the vaccination strain vaccinia virus (VACV). Knowledge about the structural ...Poxviruses are among the largest double-stranded DNA viruses, with members such as variola virus, monkeypox virus and the vaccination strain vaccinia virus (VACV). Knowledge about the structural proteins that form the viral core has remained sparse. While major core proteins have been annotated via indirect experimental evidence, their structures have remained elusive and they could not be assigned to individual core features. Hence, which proteins constitute which layers of the core, such as the palisade layer and the inner core wall, has remained enigmatic. Here we show, using a multi-modal cryo-electron microscopy (cryo-EM) approach in combination with AlphaFold molecular modeling, that trimers formed by the cleavage product of VACV protein A10 are the key component of the palisade layer. This allows us to place previously obtained descriptions of protein interactions within the core wall into perspective and to provide a detailed model of poxvirus core architecture. Importantly, we show that interactions within A10 trimers are likely generalizable over members of orthopox- and parapoxviruses. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17414.map.gz | 145.8 MB | EMDB map data format | |
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Header (meta data) | emd-17414-v30.xml emd-17414.xml | 12.1 KB 12.1 KB | Display Display | EMDB header |
Images | emd_17414.png | 218.8 KB | ||
Filedesc metadata | emd-17414.cif.gz | 4.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17414 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17414 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_17414.map.gz / Format: CCP4 / Size: 162.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | IsoNet corrected cryo-electron tomogram of isolated Vaccinia Virus cores | ||||||||||||||||||||
Voxel size | X=Y=Z: 11.048 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Vaccinia virus Western Reserve
Entire | Name: Vaccinia virus Western Reserve |
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Components |
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-Supramolecule #1: Vaccinia virus Western Reserve
Supramolecule | Name: Vaccinia virus Western Reserve / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: Purified viral cores from HeLa cells infected with Vaccinia Virus Western Reserve. NCBI-ID: 696871 / Sci species name: Vaccinia virus Western Reserve / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 9 / Component - Concentration: 1.0 mM / Component - Formula: Tris-HClTris / Component - Name: Tris hydrochloride Details: diluted 1:1 with 0.25% Trypsin (final concentration 0.125%) and 1:1 4% paraformaldehyde (final concentration 2%) in 1 mM Tris-HCl. |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 180 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K / Instrument: LEICA EM GP / Details: Leica GP2. |
Details | intact and disrupted viral cores |
Sectioning | Other: NO SECTIONING |
Fiducial marker | Manufacturer: Aurion Immuno Gold Reagents / Diameter: 10 nm |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.361 µm / Nominal defocus min: 2.361 µm / Nominal magnification: 64000 |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Details | Cryo-electron tomography data was collected with the SerialEM software package version 3.8 (Mastronarde 2005). New gain reference images were collected before data acquisition. DigitalMicrograph 3.4.3 as integrated into the Gatan Microscopy Suite v3.3 (Gatan) was used for filter tuning and SerialEM for microscope tuning. |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Average electron dose: 158.0 e/Å2 / Details: Images were collected in movie-mode with 10 frames |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: BACK PROJECTION / Software - Name: IMOD / Software - details: IsoNET 0.2 / Details: Tomogram was cropped and IsoNET corrected / Number images used: 43 |
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