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Yorodumi- EMDB-15602: In situ subtomogram average of Vaccinia virus (WR) D13 lattice, o... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15602 | |||||||||
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Title | In situ subtomogram average of Vaccinia virus (WR) D13 lattice, on immature virions | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Poxvirus rifampicin-resistance / Poxvirus rifampicin resistance protein / response to antibiotic / identical protein binding / membrane / Scaffold protein OPG125 Function and homology information | |||||||||
Biological species | Vaccinia virus WR | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 19.2 Å | |||||||||
Authors | Calcraft T / Hernandez-Gonzalez M / Nans A / Rosenthal PB / Way M | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: PLoS Biol / Year: 2023 Title: A succession of two viral lattices drives vaccinia virus assembly. Authors: Miguel Hernandez-Gonzalez / Thomas Calcraft / Andrea Nans / Peter B Rosenthal / Michael Way / Abstract: During its cytoplasmic replication, vaccinia virus assembles non-infectious spherical immature virions (IV) coated by a viral D13 lattice. Subsequently, IV mature into infectious brick-shaped ...During its cytoplasmic replication, vaccinia virus assembles non-infectious spherical immature virions (IV) coated by a viral D13 lattice. Subsequently, IV mature into infectious brick-shaped intracellular mature virions (IMV) that lack D13. Here, we performed cryo-electron tomography (cryo-ET) of frozen-hydrated vaccinia-infected cells to structurally characterise the maturation process in situ. During IMV formation, a new viral core forms inside IV with a wall consisting of trimeric pillars arranged in a new pseudohexagonal lattice. This lattice appears as a palisade in cross-section. As maturation occurs, which involves a 50% reduction in particle volume, the viral membrane becomes corrugated as it adapts to the newly formed viral core in a process that does not appear to require membrane removal. Our study suggests that the length of this core is determined by the D13 lattice and that the consecutive D13 and palisade lattices control virion shape and dimensions during vaccinia assembly and maturation. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15602.map.gz | 24.8 MB | EMDB map data format | |
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Header (meta data) | emd-15602-v30.xml emd-15602.xml | 16.2 KB 16.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15602_fsc.xml | 7 KB | Display | FSC data file |
Images | emd_15602.png | 125 KB | ||
Masks | emd_15602_msk_1.map | 27 MB | Mask map | |
Others | emd_15602_half_map_1.map.gz emd_15602_half_map_2.map.gz | 19.7 MB 19.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15602 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15602 | HTTPS FTP |
-Validation report
Summary document | emd_15602_validation.pdf.gz | 702.7 KB | Display | EMDB validaton report |
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Full document | emd_15602_full_validation.pdf.gz | 702.2 KB | Display | |
Data in XML | emd_15602_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | emd_15602_validation.cif.gz | 17.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15602 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15602 | HTTPS FTP |
-Related structure data
Related structure data | 8arhMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_15602.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.31 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_15602_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_15602_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_15602_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Vaccinia virus WR
Entire | Name: Vaccinia virus WR |
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Components |
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-Supramolecule #1: Vaccinia virus WR
Supramolecule | Name: Vaccinia virus WR / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: A36-YdF deltaNPF1-3 deltaF11 / NCBI-ID: 10254 / Sci species name: Vaccinia virus WR / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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Host (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Scaffold protein D13
Macromolecule | Name: Scaffold protein D13 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Vaccinia virus WR / Strain: Western Reserve |
Molecular weight | Theoretical: 61.948531 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MNNTIINSLI GGDDSIKRSN VFAVDSQIPT LYMPQYISLS GVMTNDGPDN QAIASFEIRD QYITALNHLV LSLELPEVKG MGRFGYVPY VGYKCINHVS ISSCNGVIWE IEGEELYNNC INNTIALKHS GYSSELNDIS IGLTPNDTIK EPSTVYVYIK T PFDVEDTF ...String: MNNTIINSLI GGDDSIKRSN VFAVDSQIPT LYMPQYISLS GVMTNDGPDN QAIASFEIRD QYITALNHLV LSLELPEVKG MGRFGYVPY VGYKCINHVS ISSCNGVIWE IEGEELYNNC INNTIALKHS GYSSELNDIS IGLTPNDTIK EPSTVYVYIK T PFDVEDTF SSLKLSDSKI TVTVTFNPVS DIVIRDSSFD FETFNKEFVY VPELSFIGYM VKNVQIKPSF IEKPRRVIGQ IN QPTATVT EVHAATSLSV YTKPYYGNTD NKFISYPGYS QDEKDYIDAY VSRLLDDLVI VSDGPPTGYP ESAEIVEVPE DGI VSIQDA DVYVKIDNVP DNMSVYLHTN LLMFGTRKNS FIYNISKKFS AITGTYSDAT KRTIFAHISH SINIIDTSIP VSLW TSQRN VYNGDNRSAE SKAKDLFIND PFIKGIDFKN KTDIISRLEV RFGNDVLYSE NGPISRIYNE LLTKSNNGTR TLTFN FTPK IFFRPTTITA NVSRGKDKLS VRVVYSTMDV NHPIYYVQKQ LVVVCNDLYK VSYDQGVSIT KIMGDNN |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Average electron dose: 1.7 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 8.0 µm / Nominal defocus min: 8.0 µm / Nominal magnification: 11600 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |