+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15694 | |||||||||
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Title | Human adenovirus type 5 lacking core protein V | |||||||||
Map data | Human adenovirus type 5 lacking core protein V | |||||||||
Sample |
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Keywords | HAdV-C5 / deltaV / VIRUS | |||||||||
Biological species | Ad5 deltaV (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||
Authors | Hernando-Perez M / San Martin C / Martin-Gonzalez N / Gomez-Gonzalez A / Bauer M / Greber UF / de Pablo PJ | |||||||||
Funding support | Spain, 1 items
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Citation | Journal: Sci Adv / Year: 2023 Title: Adenovirus core protein V reinforces the capsid and enhances genome release from disrupted particles. Authors: Natalia Martín-González / Alfonso Gómez-González / Mercedes Hernando-Pérez / Michael Bauer / Urs F Greber / Carmen San Martín / Pedro J de Pablo / Abstract: Out of the three core proteins in human adenovirus, protein V is believed to connect the inner capsid surface to the outer genome layer. Here, we explored mechanical properties and in vitro ...Out of the three core proteins in human adenovirus, protein V is believed to connect the inner capsid surface to the outer genome layer. Here, we explored mechanical properties and in vitro disassembly of particles lacking protein V (Ad5-ΔV). Ad5-ΔV particles were softer and less brittle than the wild-type ones (Ad5-wt), but they were more prone to release pentons under mechanical fatigue. In Ad5-ΔV, core components did not readily diffuse out of partially disrupted capsids, and the core appeared more condensed than in Ad5-wt. These observations suggest that instead of condensing the genome, protein V antagonizes the condensing action of the other core proteins. Protein V provides mechanical reinforcement and facilitates genome release by keeping DNA connected to capsid fragments that detach during disruption. This scenario is in line with the location of protein V in the virion and its role in Ad5 cell entry. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15694.map.gz | 882.1 MB | EMDB map data format | |
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Header (meta data) | emd-15694-v30.xml emd-15694.xml | 15.7 KB 15.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15694_fsc.xml | 18.7 KB | Display | FSC data file |
Images | emd_15694.png | 243.8 KB | ||
Others | emd_15694_half_map_1.map.gz emd_15694_half_map_2.map.gz | 801.5 MB 801.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15694 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15694 | HTTPS FTP |
-Validation report
Summary document | emd_15694_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_15694_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_15694_validation.xml.gz | 29.7 KB | Display | |
Data in CIF | emd_15694_validation.cif.gz | 40 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15694 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15694 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_15694.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Human adenovirus type 5 lacking core protein V | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.025 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half2 map in the same coordinate space as the primary map
File | emd_15694_half_map_1.map | ||||||||||||
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Annotation | Half2 map in the same coordinate space as the primary map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half1 map in the same coordinate space as the primary map
File | emd_15694_half_map_2.map | ||||||||||||
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Annotation | Half1 map in the same coordinate space as the primary map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Ad5 deltaV
Entire | Name: Ad5 deltaV (virus) |
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Components |
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-Supramolecule #1: Ad5 deltaV
Supramolecule | Name: Ad5 deltaV / type: virus / ID: 1 / Parent: 0 Details: Deletion mutant described in https://doi.org/10.1126/sciadv.abl7150 NCBI-ID: 129951 / Sci species name: Ad5 deltaV / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 150 MDa |
Virus shell | Shell ID: 1 / Diameter: 950.0 Å / T number (triangulation number): 25 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 Component:
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Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM CPC |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-50 / Number grids imaged: 1 / Number real images: 2106 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 3.442 µm / Calibrated defocus min: 0.483 µm / Calibrated magnification: 73000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 73000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |