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Yorodumi- EMDB-1574: C-terminal domain of adenovirus serotype 5 protein IX assemble in... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1574 | |||||||||
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Title | C-terminal domain of adenovirus serotype 5 protein IX assemble into an anti-parallel structure | |||||||||
Map data | SY12 modified adenovirus 5 | |||||||||
Sample |
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Keywords | adenovirus / proteinIX | |||||||||
Biological species | Human adenovirus 5 | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 11.0 Å | |||||||||
Authors | Fabry CMS / Rosa-Calatrava M / Moriscot C / Ruigrok RWH / Boulanger P / Schoehn G | |||||||||
Citation | Journal: J Virol / Year: 2009 Title: The C-terminal domains of adenovirus serotype 5 protein IX assemble into an antiparallel structure on the facets of the capsid. Authors: Céline M S Fabry / Manuel Rosa-Calatrava / Christine Moriscot / Rob W H Ruigrok / Pierre Boulanger / Guy Schoehn / Abstract: Adenovirus serotype 5 protein IX (pIX) has two domains connected by a flexible linker. Three N-terminal domains form triskelions on the capsid facets that cement hexons together, and the C-terminal ...Adenovirus serotype 5 protein IX (pIX) has two domains connected by a flexible linker. Three N-terminal domains form triskelions on the capsid facets that cement hexons together, and the C-terminal domains of four monomers form complexes toward the facet periphery. Here we present a cryoelectron microscopy structure of recombinant adenovirus with a peptide tag added to the C terminus of pIX. The structure, made up by several C termini of pIX, is longer at both ends than the wild-type protein, and Fabs directed against the tag bind to both ends of the oligomer, demonstrating that the pIX C termini associate in an antiparallel manner. | |||||||||
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_1574.map.gz | 72.9 MB | EMDB map data format | |
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Header (meta data) | emd-1574-v30.xml emd-1574.xml | 8.8 KB 8.8 KB | Display Display | EMDB header |
Images | EMD-1574.png | 796.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1574 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1574 | HTTPS FTP |
-Validation report
Summary document | emd_1574_validation.pdf.gz | 344.9 KB | Display | EMDB validaton report |
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Full document | emd_1574_full_validation.pdf.gz | 344.1 KB | Display | |
Data in XML | emd_1574_validation.xml.gz | 7.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1574 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1574 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1574.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | SY12 modified adenovirus 5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.33 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 : SY12 modified adenovirus 5
Entire | Name: SY12 modified adenovirus 5 |
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Components |
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-Supramolecule #1000: SY12 modified adenovirus 5
Supramolecule | Name: SY12 modified adenovirus 5 / type: sample / ID: 1000 Details: dodecapeptide TAYSSYMKGGKF (abbreviated SY12 ) fused to the C-terminus of pIX and a recombinant Ad5LacZ-pIX-SY12 vector has been constructed Number unique components: 1 |
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-Supramolecule #1: Human adenovirus 5
Supramolecule | Name: Human adenovirus 5 / type: virus / ID: 1 / Name.synonym: adenovirus / NCBI-ID: 28285 / Sci species name: Human adenovirus 5 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No / Syn species name: adenovirus |
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Host (natural) | Organism: Homo sapiens (human) / synonym: VERTEBRATES |
Virus shell | Shell ID: 1 / Diameter: 1000 Å / T number (triangulation number): 25 |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1. mg/mL |
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Buffer | pH: 7.5 / Details: 20mM NaCl, 10mM Tris-HCL |
Staining | Type: NEGATIVE / Details: Cryo EM |
Grid | Details: quantifoil r2/2 |
Vitrification | Cryogen name: ETHANE / Instrument: OTHER / Details: Vitrification instrument: zeiss / Method: Blot for 2 seconds before plunging |
-Electron microscopy
Microscope | JEOL 2010F |
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Alignment procedure | Legacy - Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 18 / Average electron dose: 9 e/Å2 / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 1.4 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 30000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: OTHER |
-Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: FSC 0.33 CUT-OFF / Software - Name: pft2 em3dr2 / Number images used: 2943 |