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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-23202 | |||||||||
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Title | The genome-containing AAV11 capsid | |||||||||
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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 / ![]() ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | 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 | ![]() | 588.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.8 KB 9.8 KB | Display Display | ![]() |
Images | ![]() | 299 KB | ||
Filedesc metadata | ![]() | 5.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7l6eMC ![]() 7l5qC ![]() 7l5uC ![]() 7l6aC ![]() 7l6bC ![]() 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: 0.851 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 11
Entire | Name: ![]() ![]() |
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Components |
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-Supramolecule #1: Adeno-associated virus 11
Supramolecule | Name: Adeno-associated virus 11 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 202812 / Sci species name: Adeno-associated virus 11 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No |
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-Macromolecule #1: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 58.395535 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: DGVGNASGDW HCDSTWSEGK VTTTSTRTWV LPTYNNHLYL RLGTTSSSNT YNGFSTPWGY FDFNRFHCHF SPRDWQRLIN NNWGLRPKA MRVKIFNIQV KEVTTSNGET TVANNLTSTV QIFADSSYEL PYVMDAGQEG SLPPFPNDVF MVPQYGYCGI V TGENQNQT ...String: DGVGNASGDW HCDSTWSEGK VTTTSTRTWV LPTYNNHLYL RLGTTSSSNT YNGFSTPWGY FDFNRFHCHF SPRDWQRLIN NNWGLRPKA MRVKIFNIQV KEVTTSNGET TVANNLTSTV QIFADSSYEL PYVMDAGQEG SLPPFPNDVF MVPQYGYCGI V TGENQNQT DRNAFYCLEY FPSQMLRTGN NFEMAYNFEK VPFHSMYAHS QSLDRLMNPL LDQYLWHLQS TTSGETLNQG NA ATTFGKI RSGDFAFYRK NWLPGPCVKQ QRFSKTASQN YKIPASGGNA LLKYDTHYTL NNRWSNIAPG PPMATAGPSD GDF SNAQLI FPGPSVTGNT TTSANNLLFT SEEEIAATNP RDTDMFGQIA DNNQNATTAP ITGNVTAMGV LPGMVWQNRD IYYQ GPIWA KIPHADGHFH PSPLIGGFGL KHPPPQIFIK NTPVPANPAT TFTAARVDSF ITQYSTGQVA VQIEWEIEKE RSKRW NPEV QFTSNYGNQS SMLWAPDTTG KYTEPRVIGS RYLTNHL UniProtKB: ![]() |
-Macromolecule #2: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
Macromolecule | Name: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / type: ligand / ID: 2 / Number of copies: 60 / Formula: D5M |
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Molecular weight | Theoretical: 331.222 Da |
Chemical component information | ![]() ChemComp-D5M: |
-Experimental details
-Structure determination
Method | ![]() |
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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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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
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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Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: RANDOM ASSIGNMENT |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 10429 |