+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11594 | |||||||||||||||
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Title | The structure of HAdV-D56 in complex with CD46 | |||||||||||||||
Map data | Full unmasked map | |||||||||||||||
Sample |
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Biological species | Homo sapiens (human) / Human adenovirus 56 | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.11 Å | |||||||||||||||
Authors | Rafie K / Carlson L-A | |||||||||||||||
Funding support | European Union, Sweden, 4 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2021 Title: Human species D adenovirus hexon capsid protein mediates cell entry through a direct interaction with CD46. Authors: B David Persson / Lijo John / Karim Rafie / Michael Strebl / Lars Frängsmyr / Monika Z Ballmann / Katja Mindler / Menzo Havenga / Angelique Lemckert / Thilo Stehle / Lars-Anders Carlson / Niklas Arnberg / Abstract: Human adenovirus species D (HAdV-D) types are currently being explored as vaccine vectors for coronavirus disease 2019 (COVID-19) and other severe infectious diseases. The efficacy of such vector- ...Human adenovirus species D (HAdV-D) types are currently being explored as vaccine vectors for coronavirus disease 2019 (COVID-19) and other severe infectious diseases. The efficacy of such vector-based vaccines depends on functional interactions with receptors on host cells. Adenoviruses of different species are assumed to enter host cells mainly by interactions between the knob domain of the protruding fiber capsid protein and cellular receptors. Using a cell-based receptor-screening assay, we identified CD46 as a receptor for HAdV-D56. The function of CD46 was validated in infection experiments using cells lacking and overexpressing CD46, and by competition infection experiments using soluble CD46. Remarkably, unlike HAdV-B types that engage CD46 through interactions with the knob domain of the fiber protein, HAdV-D types infect host cells through a direct interaction between CD46 and the hexon protein. Soluble hexon proteins (but not fiber knob) inhibited HAdV-D56 infection, and surface plasmon analyses demonstrated that CD46 binds to HAdV-D hexon (but not fiber knob) proteins. Cryoelectron microscopy analysis of the HAdV-D56 virion-CD46 complex confirmed the interaction and showed that CD46 binds to the central cavity of hexon trimers. Finally, soluble CD46 inhibited infection by 16 out of 17 investigated HAdV-D types, suggesting that CD46 is an important receptor for a large group of adenoviruses. In conclusion, this study identifies a noncanonical entry mechanism used by human adenoviruses, which adds to the knowledge of adenovirus biology and can also be useful for development of adenovirus-based vaccine vectors. | |||||||||||||||
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_11594.map.gz | 5.7 GB | EMDB map data format | |
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Header (meta data) | emd-11594-v30.xml emd-11594.xml | 17.9 KB 17.9 KB | Display Display | EMDB header |
Images | emd_11594.png | 108.4 KB | ||
Others | emd_11594_half_map_1.map.gz emd_11594_half_map_2.map.gz | 5.7 GB 5.7 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11594 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11594 | HTTPS FTP |
-Validation report
Summary document | emd_11594_validation.pdf.gz | 483 KB | Display | EMDB validaton report |
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Full document | emd_11594_full_validation.pdf.gz | 482.2 KB | Display | |
Data in XML | emd_11594_validation.xml.gz | 30 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11594 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11594 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_11594.map.gz / Format: CCP4 / Size: 6.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Full unmasked map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.042 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Half map 2
File | emd_11594_half_map_1.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_11594_half_map_2.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human adenovirus 56
Entire | Name: Human adenovirus 56 |
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Components |
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-Supramolecule #1: Human adenovirus 56
Supramolecule | Name: Human adenovirus 56 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 880565 / Sci species name: Human adenovirus 56 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Homo sapiens (human) |
Virus shell | Shell ID: 1 / Name: Human Adenovirus Serotype D 56 / Diameter: 1000.0 Å |
-Supramolecule #2: CD46 complement regulatory protein
Supramolecule | Name: CD46 complement regulatory protein / type: complex / ID: 2 / Parent: 1 Details: reombinantely expressed CD46 purchased from Sino Biological Inc (Cat#: 12239-H08H). |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293 |
Molecular weight | Experimental: 60 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3.6 mg/mL |
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Buffer | pH: 7.4 Details: Commercial PBS buffer stock. Medicargo, PBS tablets, 09-9400-100 |
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.037 kPa |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV |
Details | 60 uL of HadV-D56 at 1.2 mg/mL was combined with 60 uL of a 0.5 mg/mL solution of recombinant CD46, incubated on ice for 15 minutes. The sample was subsequently concentrated to a final volum of 20 uL with a nominal concentration of 3.6 and 1.5 mg/mL for HAdV-D56 and CD46, respectively. |
-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 - Frames/image: 2-20 / Average exposure time: 4.5 sec. / Average electron dose: 0.94 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -0.003 µm / Nominal defocus min: -0.0008 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |