+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18452 | |||||||||
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Title | Vaccinia virus inner core wall | |||||||||
Map data | Vaccinia virus inner core wall cryo-EM reconstruction | |||||||||
Sample |
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Keywords | Poxvirus / Vaccinia Virus / core / cryo-electron tomography / AlphaFold / VIRAL PROTEIN | |||||||||
Biological species | Vaccinia virus Western Reserve | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 20.7 Å | |||||||||
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_18452.map.gz | 31 MB | EMDB map data format | |
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Header (meta data) | emd-18452-v30.xml emd-18452.xml | 17.4 KB 17.4 KB | Display Display | EMDB header |
Images | emd_18452.png | 16.1 KB | ||
Filedesc metadata | emd-18452.cif.gz | 4.7 KB | ||
Others | emd_18452_half_map_1.map.gz emd_18452_half_map_2.map.gz | 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18452 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18452 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_18452.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Vaccinia virus inner core wall cryo-EM reconstruction | ||||||||||||||||||||
Voxel size | X=Y=Z: 2.12 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map B, Vaccinia virus inner core wall.
File | emd_18452_half_map_1.map | ||||||||||||
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Annotation | half map B, Vaccinia virus inner core wall. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map A, Vaccinia virus inner core wall.
File | emd_18452_half_map_2.map | ||||||||||||
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Annotation | half map A, Vaccinia virus inner core wall. | ||||||||||||
Projections & Slices |
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Density Histograms |
-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 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 | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 9 Component:
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 | Support film - Material: CARBON / Support film - topology: HOLEY | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K / Instrument: LEICA EM GP / Details: Leica GP2. | |||||||||
Details | Isolated viral cores with some detached soluble monodispersed particles. |
-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: 3.0 µm / Nominal defocus min: 1.25 µm / Nominal magnification: 81000 |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 9264 / Average electron dose: 53.04 e/Å2 / Details: 34 frames total. |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE / Details: ab initio without symmetry |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0) |
Final 3D classification | Software - Name: cryoSPARC (ver. 4.0) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0) |
Final reconstruction | Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 20.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 3795 |
Details | dose weighted and motion corrected |