+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21020 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | genome-containing AAVrh.39 particles | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | AAVrh.39 / capsid / genome / nucleotide binding pocket / 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 Function and homology information | |||||||||
Biological species | Adeno-associated virus / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.58 Å | |||||||||
Authors | Mietzsch M / Agbandje-McKenna M | |||||||||
Citation | Journal: J Virol / Year: 2020 Title: Comparative Analysis of the Capsid Structures of AAVrh.10, AAVrh.39, and AAV8. Authors: Mario Mietzsch / Candace Barnes / Joshua A Hull / Paul Chipman / Jun Xie / Nilakshee Bhattacharya / Duncan Sousa / Robert McKenna / Guangping Gao / Mavis Agbandje-McKenna / Abstract: Adeno-associated viruses (AAVs) from clade E are often used as vectors in gene delivery applications. This clade includes rhesus isolate 10 (AAVrh.10) and 39 (AAVrh.39) which, unlike representative ...Adeno-associated viruses (AAVs) from clade E are often used as vectors in gene delivery applications. This clade includes rhesus isolate 10 (AAVrh.10) and 39 (AAVrh.39) which, unlike representative AAV8, are capable of crossing the blood-brain barrier (BBB), thereby enabling the delivery of therapeutic genes to the central nervous system. Here, the capsid structures of AAV8, AAVrh.10 and AAVrh.39 have been determined by cryo-electron microscopy and three-dimensional image reconstruction to 3.08-, 2.75-, and 3.39-Å resolution, respectively, to enable a direct structural comparison. AAVrh.10 and AAVrh.39 are 98% identical in amino acid sequence but only ∼93.5% identical to AAV8. However, the capsid structures of all three viruses are similar, with only minor differences observed in the previously described surface variable regions, suggesting that specific residues S269 and N472, absent in AAV8, may confer the ability to cross the BBB in AAVrh.10 and AAVrh.39. Head-to-head comparison of empty and genome-containing particles showed DNA ordered in the previously described nucleotide-binding pocket, supporting the suggested role of this pocket in DNA packaging for the The structural characterization of these viruses provides a platform for future vector engineering efforts toward improved gene delivery success with respect to specific tissue targeting, transduction efficiency, antigenicity, or receptor retargeting. Recombinant adeno-associated virus vectors (rAAVs), based on AAV8 and AAVrh.10, have been utilized in multiple clinical trials to treat different monogenetic diseases. The closely related AAVrh.39 has also shown promise As recently attained for other AAV biologics, e.g., Luxturna and Zolgensma, based on AAV2 and AAV9, respectively, the vectors in this study will likely gain U.S. Food and Drug Administration approval for commercialization in the near future. This study characterized the capsid structures of these clinical vectors at atomic resolution using cryo-electron microscopy and image reconstruction for comparative analysis. The analysis suggested two key residues, S269 and N472, as determinants of BBB crossing for AAVrh.10 and AAVrh.39, a feature utilized for central nervous system delivery of therapeutic genes. The structure information thus provides a platform for engineering to improve receptor retargeting or tissue specificity. These are important challenges in the field that need attention. Capsid structure information also provides knowledge potentially applicable for regulatory product approval. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21020.map.gz | 87.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-21020-v30.xml emd-21020.xml | 10.1 KB 10.1 KB | Display Display | EMDB header |
Images | emd_21020.png | 288.6 KB | ||
Filedesc metadata | emd-21020.cif.gz | 5.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21020 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21020 | HTTPS FTP |
-Validation report
Summary document | emd_21020_validation.pdf.gz | 533.5 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_21020_full_validation.pdf.gz | 533.1 KB | Display | |
Data in XML | emd_21020_validation.xml.gz | 7.5 KB | Display | |
Data in CIF | emd_21020_validation.cif.gz | 8.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21020 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21020 | HTTPS FTP |
-Related structure data
Related structure data | 6v1zMC 0663C 6o9rC 6v10C 6v12C 6v1gC 6v1tC C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_21020.map.gz / Format: CCP4 / Size: 242.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.963 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-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: AAV8 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No |
---|
-Macromolecule #1: Capsid protein VP1
Macromolecule | Name: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Adeno-associated virus |
Molecular weight | Theoretical: 58.573527 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: GADGVGSSSG NWHCDSTWLG DRVITTSTRT WALPTYNNHL YKQISNGTSG GSTNDNTYFG YSTPWGYFDF NRFHCHFSPR DWQRLINNN WGFRPKRLNF KLFNIQVKEV TQNEGTKTIA NNLTSTIQVF TDSEYQLPYV LGSAHQGCLP PFPADVFMIP Q YGYLTLNN ...String: GADGVGSSSG NWHCDSTWLG DRVITTSTRT WALPTYNNHL YKQISNGTSG GSTNDNTYFG YSTPWGYFDF NRFHCHFSPR DWQRLINNN WGFRPKRLNF KLFNIQVKEV TQNEGTKTIA NNLTSTIQVF TDSEYQLPYV LGSAHQGCLP PFPADVFMIP Q YGYLTLNN GSQAVGRSSF YCLEYFPSQM LRTGNNFEFS YQFEDVPFHS SYAHSQSLDR LMNPLIDQYL YYLSRTQSTG GT QGTQQLL FSQAGPANMS AQAKNWLPGP CYRQQRVSTT LSQNNNSNFA WTGATKYHLN GRDSLVNPGV AMATHKDDEE RFF PSSGVL MFGKQGAGRD NVDYSSVMLT SEEEIKTTNP VATEQYGVVA DNLQQTNTGP IVGNVNSQGA LPGMVWQNRD VYLQ GPIWA KIPHTDGNFH PSPLMGGFGL KHPPPQILIK NTPVPADPPT TFSQAKLASF ITQYSTGQVS VEIEWELQKE NSKRW NPEI QYTSNYYKST NVDFAVNTEG TYSEPRPIGT RYLTRNL UniProtKB: Capsid protein VP1 |
-Macromolecule #2: DNA (5'-D(*CP*A)-3')
Macromolecule | Name: DNA (5'-D(*CP*A)-3') / type: dna / ID: 2 / Number of copies: 60 / Classification: DNA |
---|---|
Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 557.431 Da |
Sequence | String: (DC)(DA) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Average electron dose: 67.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
---|---|
Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1326 |
Initial angle assignment | Type: COMMON LINE |
Final angle assignment | Type: COMMON LINE |