+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23205 | |||||||||
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Title | The empty AAV13 capsid | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Icosahedral Capsid / AAV13 / 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 / Capsid protein Function and homology information | |||||||||
Biological species | Adeno-associated virus 13 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.76 Å | |||||||||
Authors | Mietzsch M / Agbandje-McKenna M | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Viruses / Year: 2021 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23205.map.gz | 262.9 MB | EMDB map data format | |
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Header (meta data) | emd-23205-v30.xml emd-23205.xml | 9.4 KB 9.4 KB | Display Display | EMDB header |
Images | emd_23205.png | 307.6 KB | ||
Filedesc metadata | emd-23205.cif.gz | 5.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23205 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23205 | HTTPS FTP |
-Validation report
Summary document | emd_23205_validation.pdf.gz | 698.1 KB | Display | EMDB validaton report |
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Full document | emd_23205_full_validation.pdf.gz | 697.7 KB | Display | |
Data in XML | emd_23205_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | emd_23205_validation.cif.gz | 8.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23205 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23205 | HTTPS FTP |
-Related structure data
Related structure data | 7l6iMC 7l5qC 7l5uC 7l6aC 7l6bC 7l6eC 7l6fC 7l6hC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23205.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.077 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Adeno-associated virus 13
Entire | Name: Adeno-associated virus 13 |
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Components |
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-Supramolecule #1: Adeno-associated virus 13
Supramolecule | Name: Adeno-associated virus 13 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 501327 / Sci species name: Adeno-associated virus 13 / 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: Adeno-associated virus 13 |
Molecular weight | Theoretical: 58.555508 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: ADGVGNSSGN WHCDSQWLGD RVITTSTRTW ALPTYNNHLY KQISSQSGAT NDNHYFGYST PWGYFDFNRF HCHFSPRDWQ RLINNNWGF RPKRLNFKLF NIQVKEVTQN DGTTTIANNL TSTVQVFTDS EYQLPYVLGS AHQGCLPPFP ADVFMVPQYG Y LTLNNGSQ ...String: ADGVGNSSGN WHCDSQWLGD RVITTSTRTW ALPTYNNHLY KQISSQSGAT NDNHYFGYST PWGYFDFNRF HCHFSPRDWQ RLINNNWGF RPKRLNFKLF NIQVKEVTQN DGTTTIANNL TSTVQVFTDS EYQLPYVLGS AHQGCLPPFP ADVFMVPQYG Y LTLNNGSQ AVGRSSFYCL EYFPSQMLRT GNNFQFSYTF EDVPFHSSYA HSQSLDRLMN PLIDQYLYYL NRTQTASGTQ QS RLLFSQA GPTSMSLQAK NWLPGPCYRQ QRLSKQANDN NNSNFPWTGA TKYHLNGRDS LVNPGPAMAS HKDDKEKFFP MHG TLIFGK EGTNANNADL ENVMITDEEE IRTTNPVATE QYGTVSNNLQ NSNAGPTTGT VNHQGALPGM VWQDRDVYLQ GPIW AKIPH TDGHFHPSPL MGGFGLKHPP PQIMIKNTPV PANPPTNFSA AKFASFITQY STGQVSVEIE WELQKENSKR WNPEI QYTS NYNKSVNVDF TVDTNGVYSE PRPIGTRYLT RNL UniProtKB: Capsid protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 56962 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: RANDOM ASSIGNMENT |