+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3599 | |||||||||
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Title | Snake Adenovirus type 1 | |||||||||
Map data | Snake Adenovirus type 1 | |||||||||
Sample | Snake Adenovirus type 1 != Snake adenovirus 1 Snake Adenovirus type 1
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Biological species | Snake adenovirus 1 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 10.9 Å | |||||||||
Authors | San Martin C / Menendez-Conejero R | |||||||||
Citation | Journal: Structure / Year: 2017 Title: Structure of a Reptilian Adenovirus Reveals a Phage Tailspike Fold Stabilizing a Vertebrate Virus Capsid. Authors: Rosa Menéndez-Conejero / Thanh H Nguyen / Abhimanyu K Singh / Gabriela N Condezo / Rachel E Marschang / Mark J van Raaij / Carmen San Martín / Abstract: Although non-human adenoviruses (AdVs) might offer solutions to problems posed by human AdVs as therapeutic vectors, little is known about their basic biology. In particular, there are no structural ...Although non-human adenoviruses (AdVs) might offer solutions to problems posed by human AdVs as therapeutic vectors, little is known about their basic biology. In particular, there are no structural studies on the complete virion of any AdV with a non-mammalian host. We combine mass spectrometry, cryo-electron microscopy, and protein crystallography to characterize the composition and structure of a snake AdV (SnAdV-1, Atadenovirus genus). SnAdV-1 particles contain the genus-specific proteins LH3, p32k, and LH2, a previously unrecognized structural component. Remarkably, the cementing protein LH3 has a trimeric β helix fold typical of bacteriophage host attachment proteins. The organization of minor coat proteins differs from that in human AdVs, correlating with higher thermostability in SnAdV-1. These findings add a new piece to the intriguing puzzle of virus evolution, hint at the use of cell entry pathways different from those in human AdVs, and will help development of new, thermostable SnAdV-1-based 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_3599.map.gz | 232.6 MB | EMDB map data format | |
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Header (meta data) | emd-3599-v30.xml emd-3599.xml | 10 KB 10 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3599_fsc.xml | 14.4 KB | Display | FSC data file |
Images | emd_3599.png | 156.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3599 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3599 | HTTPS FTP |
-Validation report
Summary document | emd_3599_validation.pdf.gz | 343.3 KB | Display | EMDB validaton report |
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Full document | emd_3599_full_validation.pdf.gz | 342.4 KB | Display | |
Data in XML | emd_3599_validation.xml.gz | 13.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3599 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3599 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3599.map.gz / Format: CCP4 / Size: 259.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Snake Adenovirus type 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.75 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Snake Adenovirus type 1
Entire | Name: Snake Adenovirus type 1 |
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Components |
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-Supramolecule #1: Snake adenovirus 1
Supramolecule | Name: Snake adenovirus 1 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 189830 / Sci species name: Snake adenovirus 1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Virus shell | Shell ID: 1 / Diameter: 940.0 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: 7.8 |
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Grid | Model: quantifoil / Material: COPPER/RHODIUM / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM CPC |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Film or detector model: KODAK SO-163 FILM / Average electron dose: 12.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 50000 |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |