[English] 日本語
![](img/lk-miru.gif)
- EMDB-20693: Adeno-associated virus strain AAVhu.37 capsid icosahedral structure -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-20693 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Adeno-associated virus strain AAVhu.37 capsid icosahedral structure | |||||||||
![]() | icosahedrally-averaged map of AAVhu.37 | |||||||||
![]() |
| |||||||||
![]() | capsid / blood-brain barrier penetration / 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 VP1![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.56 Å | |||||||||
![]() | Kaelber JT / 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 609.7 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 20.2 KB 20.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 21.9 KB | Display | ![]() |
Images | ![]() | 229 KB | ||
Filedesc metadata | ![]() | 6.6 KB | ||
Others | ![]() ![]() | 615.8 MB 615.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6u95MC ![]() 7jotC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | icosahedrally-averaged map of AAVhu.37 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.70065 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Half map: half A
File | emd_20693_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half A | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half B
File | emd_20693_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half B | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : Adeno-associated virus
Entire | Name: ![]() ![]() |
---|---|
Components |
|
-Supramolecule #1: Adeno-associated virus
Supramolecule | Name: Adeno-associated virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all Details: Virions containing GFP-encoding ssDNA were assembled in transfected HEK293T helper cells. NCBI-ID: 272636 / Sci species name: Adeno-associated virus / Sci species strain: hu.37 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
---|---|
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 VP1
Macromolecule | Name: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 81.528852 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: AADGYLPDWL EDNLSEGIRE WWDLKPGAPK PKANQQKQDD GRGLVLPGYK YLGPFNGLDK GEPVNAADAA ALEHDKAYDQ QLKAGDNPY LRYNHADAEF QERLQEDTSF GGNLGRAVFQ AKKRVLEPLG LVEEAAKTAP GKKRPVEPSP QRSPDSSTGI G KKGQQPAK ...String: AADGYLPDWL EDNLSEGIRE WWDLKPGAPK PKANQQKQDD GRGLVLPGYK YLGPFNGLDK GEPVNAADAA ALEHDKAYDQ QLKAGDNPY LRYNHADAEF QERLQEDTSF GGNLGRAVFQ AKKRVLEPLG LVEEAAKTAP GKKRPVEPSP QRSPDSSTGI G KKGQQPAK KRLNFGQTGD SESVPDPQPI GEPPAGPSGL GSGTMAAGGG APMADNNEGA DGVGSSSGNW HCDSTWLGDR VI TTSTRTW ALPTYNNHLY KQISNGTSGG STNDNTYFGY STPWGYFDFN RFHCHFSPRD WQRLINNNWG FRPKRLSFKL FNI QVKEVT QNEGTKTIAN NLTSTIQVFT DSEYQLPYVL GSAHQGCLPP FPADVFMIPQ YGYLTLNNGS QAVGRSSFYC LEYF PSQML RTGNNFEFSY TFEDVPFHSS YAHSQSLDRL MNPLIDQYLY YLSRTQSTGG TQGTQQLLFS QAGPANMSAQ AKNWL PGPC YRQQRVSTTL SQNNNSNFAW TGATKYHLNG RDSLVNPGVA MATHKDDEER FFPSSGVLMF GKQGAGRDNV DYSSVM LTS EEEIKTTNPV ATEQYGVVAD NLQQTNTGPI VGNVNSQGAL PGMVWQNRDV YLQGPIWAKI PHTDGNFHPS PLMGGFG LK HPPPQILIKN TPVPADPPTT FSQAKLASFI TQYSTGQVSV EIEWELQKEN SKRWNPEIQY TSNYYKSTNV DFAVNTEG T YSEPRPIGTR YLTRNL UniProtKB: Capsid protein VP1 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.4 Component:
Details: PBS | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.86 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.037 kPa | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: LEICA EM GP Details: Whatman #1 filter paper, 4.5s blot. 3.5 microliters specimen applied.. | ||||||||||||
Details | approx. 7*10^13 genome copies per mL |
-
Electron microscopy
Microscope | FEI TALOS ARCTICA |
---|---|
Specialist optics | Chromatic aberration corrector: none / 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: 1-25 / Number grids imaged: 1 / Average exposure time: 5.0 sec. / Average electron dose: 1.31 e/Å2 / Details: collected in superresolution mode |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 1.584 µm / Calibrated defocus min: 0.535 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 |