[English] 日本語
Yorodumi- EMDB-5424: Structure of adeno-associated virus-2 in complex with neutralizin... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5424 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of adeno-associated virus-2 in complex with neutralizing monoclonal antibody A20 | |||||||||
Map data | Reconstruction of adeno-associated virus-2 in complex with neutralizing monoclonal antibody A20 | |||||||||
Sample |
| |||||||||
Keywords | Adeno-associated virus / Antibody / A20 / Epitope / Fab / Gene therapy / Monoclonal | |||||||||
Function / homology | Function and homology information permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / host cell nucleolus / T=1 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / virion attachment to host cell / structural molecule activity Similarity search - Function | |||||||||
Biological species | Adeno-associated virus - 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.5 Å | |||||||||
Authors | McCraw DM / O'Donnell JK / Taylor KA / Stagg SM / Chapman MS | |||||||||
Citation | Journal: Virology Title: Structure of adeno-associated virus-2 in complex with neutralizing monoclonal antibody A20. Authors: Dustin M McCraw / Jason K O'Donnell / Kenneth A Taylor / Scott M Stagg / Michael S Chapman / Abstract: The use of adeno-associated virus (AAV) as a gene therapy vector is limited by the host neutralizing immune response. The cryo-electron microscopy (EM) structure at 8.5Å resolution is determined for ...The use of adeno-associated virus (AAV) as a gene therapy vector is limited by the host neutralizing immune response. The cryo-electron microscopy (EM) structure at 8.5Å resolution is determined for a complex of AAV-2 with the Fab' fragment of monoclonal antibody (MAb) A20, the most extensively characterized AAV MAb. The binding footprint is determined through fitting the cryo-EM reconstruction with a homology model following sequencing of the variable domain, and provides a structural basis for integrating diverse prior epitope mappings. The footprint extends from the previously implicated plateau to the side of the spike, and into the conserved canyon, covering a larger area than anticipated. Comparison with structures of binding and non-binding serotypes indicates that recognition depends on a combination of subtle serotype-specific features. Separation of the neutralizing epitope from the heparan sulfate cell attachment site encourages attempts to develop immune-resistant vectors that can still bind to target cells. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5424.map.gz | 30.7 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-5424-v30.xml emd-5424.xml | 11.2 KB 11.2 KB | Display Display | EMDB header |
Images | emd_5424_1.jpg | 75.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5424 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5424 | HTTPS FTP |
-Validation report
Summary document | emd_5424_validation.pdf.gz | 332.6 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_5424_full_validation.pdf.gz | 332.2 KB | Display | |
Data in XML | emd_5424_validation.xml.gz | 6.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5424 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5424 | HTTPS FTP |
-Related structure data
Related structure data | 3j1sMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_5424.map.gz / Format: CCP4 / Size: 51.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Reconstruction of adeno-associated virus-2 in complex with neutralizing monoclonal antibody A20 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.45 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Adeno-associated virus-2 in complex with neutralizing monoclonal ...
Entire | Name: Adeno-associated virus-2 in complex with neutralizing monoclonal antibody A20 |
---|---|
Components |
|
-Supramolecule #1000: Adeno-associated virus-2 in complex with neutralizing monoclonal ...
Supramolecule | Name: Adeno-associated virus-2 in complex with neutralizing monoclonal antibody A20 type: sample / ID: 1000 Oligomeric state: 60 A20 Fab's bind to one adeno-associated virus (one adeno-associated virus consists of 60 viral proteins) Number unique components: 2 |
---|---|
Molecular weight | Theoretical: 6.9 MDa |
-Supramolecule #1: Adeno-associated virus - 2
Supramolecule | Name: Adeno-associated virus - 2 / type: virus / ID: 1 / Name.synonym: AAV-2 / NCBI-ID: 10804 / Sci species name: Adeno-associated virus - 2 / Database: NCBI / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No / Syn species name: AAV-2 |
---|---|
Host (natural) | Organism: Homo sapiens (human) / synonym: VERTEBRATES |
Molecular weight | Theoretical: 3.9 MDa |
Virus shell | Shell ID: 1 / Diameter: 280 Å / T number (triangulation number): 1 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.14 mg/mL |
---|---|
Buffer | pH: 7.2 Details: 100 mM HEPES, 50 mM magnesium chloride, and 5% glycerol |
Grid | Details: 400 mesh carbon grid with holey carbon support |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: FEI VITROBOT MARK IV / Method: Blot for 2.0 seconds before plunging. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Temperature | Average: 93 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 120,000 times magnification Legacy - Electron beam tilt params: 0 |
Date | Feb 23, 2011 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 1000 (2k x 2k) / Number real images: 1503 / Average electron dose: 15 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 39775 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -4.0 µm / Nominal defocus min: -0.5 µm / Nominal magnification: 37000 |
Sample stage | Specimen holder: Nitrogen cooled / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Whole image |
---|---|
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Appion, ACE, EMAN / Number images used: 11898 |
Final two d classification | Number classes: 304 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A |
---|---|
Software | Name: RSRef |
Details | Protocol: Fixed. Anti-bumping restraints from CNS included 1LP3, Constrained icosahedral symmetry |
Refinement | Space: REAL / Overall B value: 0 Target criteria: Least-squares difference between experimental & model coulombic potential |
Output model | PDB-3j1s: |