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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-23201 | |||||||||
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Title | The empty AAV12 capsid | |||||||||
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![]() | Icosahedral Capsid / AAV12 / Adeno-associated virus / Parvovirus / Gene Therapy / 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 / VP1![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.54 Å | |||||||||
![]() | Mietzsch M / Agbandje-McKenna M | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Completion of the AAV Structural Atlas: Serotype Capsid Structures Reveals Clade-Specific Features. Authors: Mario Mietzsch / Ariana Jose / Paul Chipman / Nilakshee Bhattacharya / Nadia Daneshparvar / Robert McKenna / Mavis Agbandje-McKenna / ![]() Abstract: The capsid structures of most Adeno-associated virus (AAV) serotypes, already assigned to an antigenic clade, have been previously determined. This study reports the remaining capsid structures of ...The capsid structures of most Adeno-associated virus (AAV) serotypes, already assigned to an antigenic clade, have been previously determined. This study reports the remaining capsid structures of AAV7, AAV11, AAV12, and AAV13 determined by cryo-electron microscopy and three-dimensional image reconstruction to 2.96, 2.86, 2.54, and 2.76 Å resolution, respectively. These structures complete the structural atlas of the AAV serotype capsids. AAV7 represents the first clade D capsid structure; AAV11 and AAV12 are of a currently unassigned clade that would include AAV4; and AAV13 represents the first AAV2-AAV3 hybrid clade C capsid structure. These newly determined capsid structures all exhibit the AAV capsid features including 5-fold channels, 3-fold protrusions, 2-fold depressions, and a nucleotide binding pocket with an ordered nucleotide in genome-containing capsids. However, these structures have viral proteins that display clade-specific loop conformations. This structural characterization completes our three-dimensional library of the current AAV serotypes to provide an atlas of surface loop configurations compatible with capsid assembly and amenable for future vector engineering efforts. Derived vectors could improve gene delivery success with respect to specific tissue targeting, transduction efficiency, antigenicity or receptor retargeting. | |||||||||
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 | ![]() | 263 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.4 KB 9.4 KB | Display Display | ![]() |
Images | ![]() | 324.4 KB | ||
Filedesc metadata | ![]() | 5.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 663.9 KB | Display | ![]() |
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Full document | ![]() | 663.5 KB | Display | |
Data in XML | ![]() | 7.6 KB | Display | |
Data in CIF | ![]() | 8.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7l6bMC ![]() 7l5qC ![]() 7l5uC ![]() 7l6aC ![]() 7l6eC ![]() 7l6fC ![]() 7l6hC ![]() 7l6iC 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: 1.082 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Adeno-associated virus 12
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Adeno-associated virus 12
Supramolecule | Name: Adeno-associated virus 12 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 235458 / Sci species name: Adeno-associated virus 12 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No |
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-Macromolecule #1: VP1
Macromolecule | Name: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 58.549543 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: DGVGNASGDW HCDSTWSEGR VTTTSTRTWV LPTYNNHLYL RIGTTANSNT YNGFSTPWGY FDFNRFHCHF SPRDWQRLIN NNWGLRPKS MRVKIFNIQV KEVTTSNGET TVANNLTSTV QIFADSTYEL PYVMDAGQEG SFPPFPNDVF MVPQYGYCGV V TGKNQNQT ...String: DGVGNASGDW HCDSTWSEGR VTTTSTRTWV LPTYNNHLYL RIGTTANSNT YNGFSTPWGY FDFNRFHCHF SPRDWQRLIN NNWGLRPKS MRVKIFNIQV KEVTTSNGET TVANNLTSTV QIFADSTYEL PYVMDAGQEG SFPPFPNDVF MVPQYGYCGV V TGKNQNQT DRNAFYCLEY FPSQMLRTGN NFEVSYQFEK VPFHSMYAHS QSLDRMMNPL LDQYLWHLQS TTTGNSLNQG TA TTTYGKI TTGDFAYYRK NWLPGACIKQ QKFSKNANQN YKIPASGGDA LLKYDTHTTL NGRWSNMAPG PPMATAGAGD SDF SNSQLI FAGPNPSGNT TTSSNNLLFT SEEEIATTNP RDTDMFGQIA DNNQNATTAP HIANLDAMGI VPGMVWQNRD IYYQ GPIWA KVPHTDGHFH PSPLMGGFGL KHPPPQIFIK NTPVPANPNT TFSAARINSF LTQYSTGQVA VQIDWEIQKE HSKRW NPEV QFTSNYGTQN SMLWAPDNAG NYHELRAIGS RFLTHHL UniProtKB: VP1 |
-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 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 220137 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: RANDOM ASSIGNMENT |