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Yorodumi- EMDB-5594: Cryo-EM structure of short shafted adenovirus type 5 complexed wi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5594 | |||||||||
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Title | Cryo-EM structure of short shafted adenovirus type 5 complexed with factor VII | |||||||||
Map data | Reconstruction of adenovirus type 5 modified to have a short shafted fiber with coagulation factor VII bound | |||||||||
Sample |
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Keywords | Adenovirus / coagulation factor VII / innate immunity | |||||||||
Biological species | Human adenovirus 5 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.7 Å | |||||||||
Authors | Irons EE / Flatt JW / Doronin K / Fox TL / Sumida JP / Acchione M / Stewart PL / Shayakhmetov DM | |||||||||
Citation | Journal: J Virol / Year: 2013 Title: Coagulation factor binding orientation and dimerization may influence infectivity of adenovirus-coagulation factor complexes. Authors: Eric E Irons / Justin W Flatt / Konstantin Doronin / Tara L Fox / Mauro Acchione / Phoebe L Stewart / Dmitry M Shayakhmetov / Abstract: Adenoviruses (Ads) are promising vectors for therapeutic interventions in humans. When injected into the bloodstream, Ad vectors can bind several vitamin K-dependent blood coagulation factors, which ...Adenoviruses (Ads) are promising vectors for therapeutic interventions in humans. When injected into the bloodstream, Ad vectors can bind several vitamin K-dependent blood coagulation factors, which contributes to virus sequestration in the liver by facilitating transduction of hepatocytes. Although both coagulation factors FVII and FX bind the hexon protein of human Ad serotype 5 (HAdv5) with a very high affinity, only FX appears to play a role in mediating Ad-hepatocyte transduction in vivo. To understand the discrepancy between efficacy of FVII binding to hexon and its apparently poor capacity for supporting virus cell entry, we analyzed the HAdv5-FVII complex by using high-resolution cryo-electron microscopy (cryo-EM) followed by molecular dynamic flexible fitting (MDFF) simulations. The results indicate that although hexon amino acids T423, E424, and T425, identified earlier as critical for FX binding, are also involved in mediating binding of FVII, the FVII GLA domain sits within the surface-exposed hexon trimer depression in a different orientation from that found for FX. Furthermore, we found that when bound to hexon, two proximal FVII molecules interact via their serine protease (SP) domains and bury potential heparan sulfate proteoglycan (HSPG) receptor binding residues within the dimer interface. In contrast, earlier cryo-EM studies of the Ad-FX interaction showed no evidence of dimer formation. Dimerization of FVII bound to Ad may be a contributing mechanistic factor for the differential infectivity of Ad-FX and Ad-FVII complexes, despite high-affinity binding of both these coagulation factors to the virus. | |||||||||
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_5594.map.gz | 230.5 MB | EMDB map data format | |
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Header (meta data) | emd-5594-v30.xml emd-5594.xml | 10.3 KB 10.3 KB | Display Display | EMDB header |
Images | emd_5594.tif | 205.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5594 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5594 | HTTPS FTP |
-Validation report
Summary document | emd_5594_validation.pdf.gz | 78.3 KB | Display | EMDB validaton report |
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Full document | emd_5594_full_validation.pdf.gz | 77.4 KB | Display | |
Data in XML | emd_5594_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5594 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5594 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5594.map.gz / Format: CCP4 / Size: 976.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of adenovirus type 5 modified to have a short shafted fiber with coagulation factor VII bound | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.25 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 : Human zymogen coagulation factor VII bound to human adenovirus ty...
Entire | Name: Human zymogen coagulation factor VII bound to human adenovirus type 5 from species C. The virus has been modified to contain a short shafted fiber. |
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Components |
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-Supramolecule #1000: Human zymogen coagulation factor VII bound to human adenovirus ty...
Supramolecule | Name: Human zymogen coagulation factor VII bound to human adenovirus type 5 from species C. The virus has been modified to contain a short shafted fiber. type: sample / ID: 1000 Oligomeric state: 240 factor VII molecules bind to one Ad virion Number unique components: 2 |
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Molecular weight | Theoretical: 164 MDa |
-Supramolecule #1: Human adenovirus 5
Supramolecule | Name: Human adenovirus 5 / type: virus / ID: 1 / NCBI-ID: 28285 / Sci species name: Human adenovirus 5 / Database: NCBI / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Homo sapiens (human) / synonym: VERTEBRATES |
Virus shell | Shell ID: 2 / Name: hexon capsid / Diameter: 920 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
Concentration | 0.6 mg/mL |
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Buffer | pH: 7.6 / Details: 50mM Tris, 150mM NaCl, 2mM CaCl2, 2mM MgCl2 |
Grid | Details: Quantifoil R2/4 holey carbon grids, glow discharged |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 30 % / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER / Method: Blot for 6 seconds before plunging |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 300,000 times magnification Legacy - Electron beam tilt params: 0 |
Details | Low dose |
Date | Nov 14, 2010 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 1503 / Average electron dose: 20 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 400000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 310000 |
Sample stage | Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Details | The particles were selected with an in-house script and processed using Frealign. |
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CTF correction | Details: Each particle |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.7 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Frealign / Number images used: 837 |