+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29377 | |||||||||
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Title | AAV1 VP3 Only Capsid | |||||||||
Map data | ||||||||||
Sample |
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Keywords | AAV / gene therapy / capsid / VP3 / VIRUS LIKE PARTICLE | |||||||||
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 - 1 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.27 Å | |||||||||
Authors | Mietzsch M / McKenna R | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Mol Ther Methods Clin Dev / Year: 2023 Title: Production and characterization of an AAV1-VP3-only capsid: An analytical benchmark standard. Authors: Mario Mietzsch / Weijing Liu / Ke Ma / Antonette Bennett / Austin R Nelson / Keely Gliwa / Paul Chipman / Xiaofeng Fu / Shane Bechler / Robert McKenna / Rosa Viner / Abstract: Adeno-associated viruses (AAVs) are non-enveloped ssDNA icosahedral T = 1 viruses used as vectors for clinical gene delivery. Currently, there are over 200 AAV-related clinical trials and six ...Adeno-associated viruses (AAVs) are non-enveloped ssDNA icosahedral T = 1 viruses used as vectors for clinical gene delivery. Currently, there are over 200 AAV-related clinical trials and six approved biologics on the market. As such new analytical methods are continually being developed to characterize and monitor the quality and purity of manufactured AAV vectors, these include ion-exchange chromatography and Direct Mass Technology. However, these methods require homogeneous analytical standards with a high molecular weight standard comparable to the mass of an AAV capsid. Described here is the design, production, purification, characterization, and the cryo-electron microscopy structure of an AAV1-VP3-only capsid that fulfills this need as a calibrant to determine capsid mass, charge, homogeneity, and transgene packaging characteristics. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29377.map.gz | 345.4 MB | EMDB map data format | |
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Header (meta data) | emd-29377-v30.xml emd-29377.xml | 14 KB 14 KB | Display Display | EMDB header |
Images | emd_29377.png | 72.5 KB | ||
Filedesc metadata | emd-29377.cif.gz | 5.5 KB | ||
Others | emd_29377_half_map_1.map.gz emd_29377_half_map_2.map.gz | 114.7 MB 114.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29377 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29377 | HTTPS FTP |
-Validation report
Summary document | emd_29377_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_29377_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_29377_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | emd_29377_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29377 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29377 | HTTPS FTP |
-Related structure data
Related structure data | 8fq4MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_29377.map.gz / Format: CCP4 / Size: 371.3 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: 0.939 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_29377_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_29377_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Adeno-associated virus - 1
Entire | Name: Adeno-associated virus - 1 |
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Components |
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-Supramolecule #1: Adeno-associated virus - 1
Supramolecule | Name: Adeno-associated virus - 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 85106 / Sci species name: Adeno-associated virus - 1 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: Yes |
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Molecular weight | Theoretical: 3.57 MDa |
Virus shell | Shell ID: 1 / T number (triangulation number): 1 |
-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 - 1 |
Molecular weight | Theoretical: 58.299422 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: ADGVGNASGN WHCDSTWLGD RVITTSTRTW ALPTYNNHLY KQISSASTGA SNDNHYFGYS TPWGYFDFNR FHCHFSPRDW QRLINNNWG FRPKRLNFKL FNIQVKEVTT NDGVTTIANN LTSTVQVFSD SEYQLPYVLG SAHQGCLPPF PADVFMIPQY G YLTLNNGS ...String: ADGVGNASGN WHCDSTWLGD RVITTSTRTW ALPTYNNHLY KQISSASTGA SNDNHYFGYS TPWGYFDFNR FHCHFSPRDW QRLINNNWG FRPKRLNFKL FNIQVKEVTT NDGVTTIANN LTSTVQVFSD SEYQLPYVLG SAHQGCLPPF PADVFMIPQY G YLTLNNGS QAVGRSSFYC LEYFPSQMLR TGNNFTFSYT FEEVPFHSSY AHSQSLDRLM NPLIDQYLYY LNRTQNQSGS AQ NKDLLFS RGSPAGMSVQ PKNWLPGPCY RQQRVSKTKT DNNNSNFTWT GASKYNLNGR ESIINPGTAM ASHKDDEDKF FPM SGVMIF GKESAGASNT ALDNVMITDE EEIKATNPVA TERFGTVAVN FQSSSTDPAT GDVHAMGALP GMVWQDRDVY LQGP IWAKI PHTDGHFHPS PLMGGFGLKN PPPQILIKNT PVPANPPAEF SATKFASFIT QYSTGQVSVE IEWELQKENS KRWNP EVQY TSNYAKSANV DFTVDNNGLY TEPRPIGTRY LTRPL 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: DIRECT ELECTRON APOLLO (4k x 4k) / Average electron dose: 59.0 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 / Nominal defocus max: 1.84 µm / Nominal defocus min: 0.48 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.27 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 4418 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |