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Yorodumi- PDB-5uf6: The 2.8 A Electron Microscopy Structure of Adeno-Associated Virus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5uf6 | |||||||||
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Title | The 2.8 A Electron Microscopy Structure of Adeno-Associated Virus-DJ Bound by a Heparanoid Pentasaccharide | |||||||||
Components | capsid protein VP1 | |||||||||
Keywords | VIRUS LIKE PARTICLE / glycan / receptor / attachment | |||||||||
Function / homology | Empty Capsid Viral Protein 2 / Parvovirus coat protein VP1/VP2 / Beta Complex / Mainly Beta / fondaparinux Function and homology information | |||||||||
Biological species | Adeno-associated virus | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Xie, Q. / Spear, J.M. / Noble, A.J. / Sousa, D.R. / Meyer, N.L. / Davulcu, O. / Zhang, F. / Linhardt, R.J. / Stagg, S.M. / Chapman, M. | |||||||||
Funding support | United States, 1items
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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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5uf6.cif.gz | 123.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uf6.ent.gz | 92.3 KB | Display | PDB format |
PDBx/mmJSON format | 5uf6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uf/5uf6 ftp://data.pdbj.org/pub/pdb/validation_reports/uf/5uf6 | HTTPS FTP |
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-Related structure data
Related structure data | 8574MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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3 |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 58577.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Adeno-associated virus / Strain: hybrid of serotypes 2, 8, and 9 / Gene: CAPSID / Plasmid: pFBDDJM11 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 |
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#2: Polysaccharide | 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2- ...2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-methyl 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranoside / fondaparinux |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Adeno-associated virus / Type: VIRUS / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 3.75 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Adeno-associated virus / Strain: hybrid of serotypes 2, 8, and 9 | ||||||||||||||||||||
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) / Strain: SF9 / Plasmid: pFBDDJM11 | ||||||||||||||||||||
Details of virus | Empty: YES / Enveloped: NO / Isolate: SEROTYPE / Type: VIRUS-LIKE PARTICLE | ||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 60 viral subunits form the icosahedral capsid | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K Details: blot force = 1, blot time = 3 seconds, total blots = 1 |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 29000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 750 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1.4 sec. / Electron dose: 66 e/Å2 / Detector mode: INTEGRATING / Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Num. of grids imaged: 1 / Num. of real images: 1051 |
Image scans | Movie frames/image: 45 / Used frames/image: 1-45 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 120166 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 107454 / Symmetry type: POINT |