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Yorodumi- EMDB-2568: Human full-length coagulation factor X and its isolated GLA domai... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2568 | |||||||||
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Title | Human full-length coagulation factor X and its isolated GLA domain bind to different regions of the adenovirus serotype 5 hexon capsomer | |||||||||
Map data | Only 1/8 of the map to see the hexons | |||||||||
Sample |
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Keywords | Adenovirus / Hexon / Scavenger receptors / Factor X / GLA domain / Peptidomimetic / Vectors / Targeting | |||||||||
Biological species | synthetic construct (others) / Human adenovirus 5 | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 9.0 Å | |||||||||
Authors | Sumarheni S / Hong SS / Josserand V / Coll J-L / Boulanger P / Schoehn G / Fender P | |||||||||
Citation | Journal: Hum Gene Ther / Year: 2014 Title: Human full-length coagulation factor X and a GLA domain-derived 40-mer polypeptide bind to different regions of the adenovirus serotype 5 hexon capsomer. Authors: Sudir Sumarheni / Saw See Hong / Véronique Josserand / Jean-Luc Coll / Pierre Boulanger / Guy Schoehn / Pascal Fender / Abstract: The interaction of human adenovirus (HAdV)-C5 and many other adenoviruses with blood coagulation factors (e.g., human factor X, FX) involves the binding of their GLA domain to the hexon capsomers, ...The interaction of human adenovirus (HAdV)-C5 and many other adenoviruses with blood coagulation factors (e.g., human factor X, FX) involves the binding of their GLA domain to the hexon capsomers, resulting in high levels of hepatotropism and potential hepatotoxicity. In this study, we tested the possibility of preventing these undesirable effects by using a GLA-mimicking peptide as a competitor. An FX GLA domain-derived, 40-mer polypeptide carrying 12 carboxyglutamate residues was synthesized (GLA(mim)). Surface plasmon resistance (SPR) analysis showed that GLA(mim) reacted with free and capsid-embedded hexon with a nanomolar affinity. Unexpectedly, GLA(mim) failed to compete with FX for hexon binding, and instead significantly increased the formation of FX-hexon or FX-adenovirion complexes. This observation was confirmed by in vitro cell transduction experiments using HAdV-C5-Luciferase vector (HAdV5-Luc), as preincubation of HAdV5-Luc with GLA(mim) before FX addition resulted in a higher transgene expression compared with FX alone. HAdV-C5 virions complexed with GLA(mim) were analyzed by cryoelectron microscopy. Image reconstruction demonstrated the bona fide hexon-GLA(mim) interaction, as for the full-length FX, although with considerable differences in stoichiometry and relative location on the hexon capsomer. Three extra densities were found at the periphery of each hexon, whereas one single FX molecule occupied the central cavity of the hexon trimeric capsomer. A refined analysis indicated that each extra density is found at the expected location of one highly variable loop 1 of the hexon, involved in scavenger receptor recognition. HAdV5-Luc complexed with a bifunctional GLA(mim)RGD peptide showed a lesser hepatotropism, compared with control HAdV5-Luc alone, and efficiently targeted αβ-integrin-overexpressing tumor cells in an in vivo mouse tumor model. Collectively, our findings open new perspectives in the design of adenoviral vectors for biotherapy. | |||||||||
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_2568.map.gz | 20.3 MB | EMDB map data format | |
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Header (meta data) | emd-2568-v30.xml emd-2568.xml | 9.8 KB 9.8 KB | Display Display | EMDB header |
Images | EMD-2568.png | 431.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2568 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2568 | HTTPS FTP |
-Validation report
Summary document | emd_2568_validation.pdf.gz | 333.6 KB | Display | EMDB validaton report |
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Full document | emd_2568_full_validation.pdf.gz | 332.7 KB | Display | |
Data in XML | emd_2568_validation.xml.gz | 5.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2568 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2568 | 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_2568.map.gz / Format: CCP4 / Size: 58.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Only 1/8 of the map to see the hexons | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.26 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 : HAdV-C5 virions complexed with GLAmim
Entire | Name: HAdV-C5 virions complexed with GLAmim |
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Components |
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-Supramolecule #1000: HAdV-C5 virions complexed with GLAmim
Supramolecule | Name: HAdV-C5 virions complexed with GLAmim / type: sample / ID: 1000 / Number unique components: 2 |
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Molecular weight | Experimental: 150 MDa / Theoretical: 150 MDa |
-Supramolecule #1: Human adenovirus 5
Supramolecule | Name: Human adenovirus 5 / type: virus / ID: 1 / NCBI-ID: 28285 / Sci species name: Human adenovirus 5 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No / Sci species serotype: 5 |
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Host (natural) | Organism: Homo sapiens (human) / synonym: VERTEBRATES |
Molecular weight | Experimental: 150 MDa / Theoretical: 150 MDa |
Virus shell | Shell ID: 1 / Diameter: 1000 Å / T number (triangulation number): 25 |
-Macromolecule #1: GLAmim peptide
Macromolecule | Name: GLAmim peptide / type: ligand / ID: 1 Details: GLAmim peptide contains 12 gamma-carboxyglutamate residues and carries a biotinyl group at its C-terminal end. Number of copies: 1 / Recombinant expression: No |
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Source (natural) | Organism: synthetic construct (others) |
-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: 7.4 / Details: 10mM Hepes buffer 2 mm CaCl2 |
Staining | Type: NEGATIVE / Details: cryo |
Grid | Details: Quantifoil R2/1 holey grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Method: Blot for 2 seconds before plunging |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Date | Sep 10, 2012 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 33 / Average electron dose: 15 e/Å2 / Od range: 1 / Bits/pixel: 8 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.3 mm / Nominal defocus max: 0.004 µm / Nominal defocus min: 0.001 µm / Nominal magnification: 30000 |
Sample stage | Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Details | pft2 em3dr2 |
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CTF correction | Details: flipmix |
Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: OTHER / Software - Name: pft2, em3dr2 / Number images used: 4762 |