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Yorodumi- EMDB-1575: C-terminal domain of adenovirus serotype 5 protein IX assemble in... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1575 | |||||||||
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Title | C-terminal domain of adenovirus serotype 5 protein IX assemble into an anti-parallel structure | |||||||||
Map data | Adenovirus sy12 with anti-sy12 fab | |||||||||
Sample |
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Keywords | adenovirus / proteinIX / Fab | |||||||||
Biological species | Human adenovirus 5 | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 22.0 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_1575.map.gz | 56.2 MB | EMDB map data format | |
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Header (meta data) | emd-1575-v30.xml emd-1575.xml | 9.3 KB 9.3 KB | Display Display | EMDB header |
Images | EMD-1575.png | 701.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1575 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1575 | HTTPS FTP |
-Validation report
Summary document | emd_1575_validation.pdf.gz | 283 KB | Display | EMDB validaton report |
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Full document | emd_1575_full_validation.pdf.gz | 282.2 KB | Display | |
Data in XML | emd_1575_validation.xml.gz | 7.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1575 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1575 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1575.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Adenovirus sy12 with anti-sy12 fab | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.54 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 plus rabbit anti SY12 Fab
Entire | Name: SY12 modified adenovirus 5 plus rabbit anti SY12 Fab |
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Components |
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-Supramolecule #1000: SY12 modified adenovirus 5 plus rabbit anti SY12 Fab
Supramolecule | Name: SY12 modified adenovirus 5 plus rabbit anti SY12 Fab / 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 anti SY12 IgG have been clived into FAb using ...Details: dodecapeptide TAYSSYMKGGKF (abbreviated SY12 ) fused to the C-terminus of pIX and a recombinant Ad5LacZ-pIX-SY12 vector has been constructed anti SY12 IgG have been clived into FAb using papain and then purified. The complex have been generated using an excess of Fab 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 5 Details: anti SY12 Fab attached to the C-terminal part of adenovirus 5 protein IX 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 5 |
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Host (natural) | Organism: Homo sapiens (human) / synonym: VERTEBRATES |
Molecular weight | Experimental: 150 MDa |
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: 11 / 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
Details | Fab-adenovirus complex |
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CTF correction | Details: Each particle |
Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: FSC 0.33 CUT-OFF / Software - Name: pft2 em3dr2 / Number images used: 949 |