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- EMDB-22412: Adeno-associated virus strain AAV7 capsid icosahedral structure -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-22412 | |||||||||
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Title | Adeno-associated virus strain AAV7 capsid icosahedral structure | |||||||||
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![]() | AAV / parvovirus / Parvoviridae / adeno-associated virus / capsid / VIRUS | |||||||||
Function / homology | Phospholipase A2-like domain / Phospholipase A2-like domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus / T=1 icosahedral viral capsid / structural molecule activity / Capsid protein![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
![]() | Firlar E / Yost SA | |||||||||
![]() | ![]() Title: Structure of the AAVhu.37 capsid by cryoelectron microscopy. Authors: Jason T Kaelber / Samantha A Yost / Keith A Webber / Emre Firlar / Ye Liu / Olivier Danos / Andrew C Mercer / ![]() Abstract: Adeno-associated viruses (AAVs) are used as in vivo gene-delivery vectors in gene-therapy products and have been heavily investigated for numerous indications. Over 100 naturally occurring AAV ...Adeno-associated viruses (AAVs) are used as in vivo gene-delivery vectors in gene-therapy products and have been heavily investigated for numerous indications. Over 100 naturally occurring AAV serotypes and variants have been isolated from primate samples. Many reports have described unique properties of these variants (for instance, differences in potency, target cell or evasion of the immune response), despite high amino-acid sequence conservation. AAVhu.37 is of interest for clinical applications owing to its proficient transduction of the liver and central nervous system. The sequence identity of the AAVhu.37 VP1 to the well characterized AAVrh.10 serotype, for which no structure is available, is greater than 98%. Here, the structure of the AAVhu.37 capsid at 2.56 Å resolution obtained via single-particle cryo-electron microscopy is presented. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 106.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.8 KB 20.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 19 KB | Display | ![]() |
Images | ![]() | 252.5 KB | ||
Masks | ![]() | 600.7 MB | ![]() | |
Filedesc metadata | ![]() | 6.5 KB | ||
Others | ![]() ![]() ![]() | 398.7 MB 483.1 MB 482 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 927.2 KB | Display | ![]() |
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Full document | ![]() | 926.7 KB | Display | |
Data in XML | ![]() | 28.6 KB | Display | |
Data in CIF | ![]() | 36.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7jotMC ![]() 6u95C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.72267 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_22412_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_22412_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_22412_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Adeno-associated virus - 7
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Adeno-associated virus - 7
Supramolecule | Name: Adeno-associated virus - 7 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all Details: Virions containing GFP-encoding ssDNA were assembled in transfected HEK293T helper cells. NCBI-ID: 202812 / Sci species name: Adeno-associated virus - 7 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: ![]() |
Molecular weight | Theoretical: 5 MDa |
Virus shell | Shell ID: 1 / Diameter: 250.0 Å / T number (triangulation number): 1 |
-Macromolecule #1: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 58.438547 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: DGVGNASGNW HCDSTWLGDR VITTSTRTWA LPTYNNHLYK QISSETAGST NDNTYFGYST PWGYFDFNRF HCHFSPRDWQ RLINNNWGF RPKKLRFKLF NIQVKEVTTN DGVTTIANNL TSTIQVFSDS EYQLPYVLGS AHQGCLPPFP ADVFMIPQYG Y LTLNNGSQ ...String: DGVGNASGNW HCDSTWLGDR VITTSTRTWA LPTYNNHLYK QISSETAGST NDNTYFGYST PWGYFDFNRF HCHFSPRDWQ RLINNNWGF RPKKLRFKLF NIQVKEVTTN DGVTTIANNL TSTIQVFSDS EYQLPYVLGS AHQGCLPPFP ADVFMIPQYG Y LTLNNGSQ SVGRSSFYCL EYFPSQMLRT GNNFEFSYSF EDVPFHSSYA HSQSLDRLMN PLIDQYLYYL ARTQSNPGGT AG NRELQFY QGGPSTMAEQ AKNWLPGPCF RQQRVSKTLD QNNNSNFAWT GATKYHLNGR NSLVNPGVAM ATHKDDEDRF FPS SGVLIF GKTGATNKTT LENVLMTNEE EIRPTNPVAT EEYGIVSSNL QAANTAAQTQ VVNNQGALPG MVWQNRDVYL QGPI WAKIP HTDGNFHPSP LMGGFGLKHP PPQILIKNTP VPANPPEVFT PAKFASFITQ YSTGQVSVEI EWELQKENSK RWNPE IQYT SNFEKQTGVD FAVDSQGVYS EPRPIGTRYL TRNL UniProtKB: Capsid protein |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 Component:
Details: PBS | ||||||||||||
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Grid | Model: Quantifoil / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.286 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.037 kPa | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: LEICA EM GP / Details: Whatman #1 filter paper. | ||||||||||||
Details | approx. 8*10^14 genome copies per mL |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-30 / Number grids imaged: 1 / Number real images: 2430 / Average exposure time: 6.0 sec. / Average electron dose: 1.064 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.836 µm / Calibrated defocus min: 0.244 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |