[English] 日本語
Yorodumi- EMDB-8574: Single particle reconstruction of chimeric adeno-associated virus... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8574 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Single particle reconstruction of chimeric adeno-associated virus-DJ with a Heparanoid Pentasaccharide | |||||||||
Map data | chimeric adeno-associated virus-DJ with a Heparanoid Pentasaccharide | |||||||||
Sample |
| |||||||||
Biological species | Adeno-associated virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Xie Q / Noble AJ / Sousa DR / Meyer NL / Davulcu O / Zhang FM / Linhardt RJ / Stagg SM / Chapman MS | |||||||||
Funding support | United States, 1 items
| |||||||||
Citation | Journal: Mol Ther Methods Clin Dev / Year: 2017 Title: The 2.8 Å Electron Microscopy Structure of Adeno-Associated Virus-DJ Bound by a Heparinoid Pentasaccharide. Authors: Qing Xie / John M Spear / Alex J Noble / Duncan R Sousa / Nancy L Meyer / Omar Davulcu / Fuming Zhang / Robert J Linhardt / Scott M Stagg / Michael S Chapman / Abstract: Atomic structures of adeno-associated virus (AAV)-DJ, alone and in complex with fondaparinux, have been determined by cryoelectron microscopy at 3 Å resolution. The gene therapy vector, AAV-DJ, is ...Atomic structures of adeno-associated virus (AAV)-DJ, alone and in complex with fondaparinux, have been determined by cryoelectron microscopy at 3 Å resolution. The gene therapy vector, AAV-DJ, is a hybrid of natural serotypes that was previously derived by directed evolution, selecting for hepatocyte entry and resistance to neutralization by human serum. The structure of AAV-DJ differs from that of parental serotypes in two regions where neutralizing antibodies bind, so immune escape appears to have been the primary driver of AAV-DJ's directed evolution. Fondaparinux is an analog of cell surface heparan sulfate to which several AAVs bind during entry. Fondaparinux interacts with viral arginines at a known heparin binding site, without the large conformational changes whose presence was controversial in low-resolution imaging of AAV2-heparin complexes. The glycan density suggests multi-modal binding that could accommodate sequence variation and multivalent binding along a glycan polymer, consistent with a role in attachment, prior to more specific interactions with a receptor protein mediating entry. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8574.map.gz | 67.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-8574-v30.xml emd-8574.xml | 17.7 KB 17.7 KB | Display Display | EMDB header |
Images | emd_8574.png | 628.7 KB | ||
Others | emd_8574_additional_1.map.gz emd_8574_additional_2.map.gz | 66.6 MB 68.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8574 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8574 | HTTPS FTP |
-Validation report
Summary document | emd_8574_validation.pdf.gz | 423 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_8574_full_validation.pdf.gz | 422.5 KB | Display | |
Data in XML | emd_8574_validation.xml.gz | 6.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8574 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8574 | HTTPS FTP |
-Related structure data
Related structure data | 5uf6MC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_8574.map.gz / Format: CCP4 / Size: 76.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | chimeric adeno-associated virus-DJ with a Heparanoid Pentasaccharide | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2159 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Additional map: Adeno-Associated Virus-DJ Bound by a Heparanoid Pentasaccharide, native...
File | emd_8574_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Adeno-Associated Virus-DJ Bound by a Heparanoid Pentasaccharide, native map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Adeno-Associated Virus-DJ Bound by a Heparanoid Pentasaccharide, difference...
File | emd_8574_additional_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Adeno-Associated Virus-DJ Bound by a Heparanoid Pentasaccharide, difference map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Adeno-associated virus
Entire | Name: Adeno-associated virus |
---|---|
Components |
|
-Supramolecule #1: Adeno-associated virus
Supramolecule | Name: Adeno-associated virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 272636 / Sci species name: Adeno-associated virus / Sci species strain: hybrid of serotypes 2, 8, and 9 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: Yes |
---|---|
Host system | Organism: Spodoptera frugiperda (fall armyworm) / Recombinant strain: SF9 / Recombinant plasmid: pFBDDJM11 |
Molecular weight | Theoretical: 3.75 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.60 mg/mL | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.4 Component:
| ||||||||||||
Grid | Model: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: blot force = 1, blot time = 3 seconds, total blots = 1. | ||||||||||||
Details | 60 viral subunits form the icosahedral capsid |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Detector mode: INTEGRATING / Digitization - Frames/image: 1-45 / Number grids imaged: 1 / Number real images: 1051 / Average exposure time: 1.4 sec. / Average electron dose: 66.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 29000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |