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- EMDB-49739: The AAVpo.6 capsid -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-49739
TitleThe AAVpo.6 capsid
Map data
Sample
  • Virus: Adeno-associated virus
    • Protein or peptide: Capsid protein VP1
KeywordsAAVpo.6 / porcine adeno-associated virus / gene therapy / vector / cryo-EM / VIRUS
Function / homologyPhospholipase 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 speciesAdeno-associated virus
Methodsingle particle reconstruction / cryo EM / Resolution: 1.77 Å
AuthorsNelson A / Mietzsch M / McKenna R
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082946 United States
CitationJournal: Viruses / Year: 2025
Title: Structural and Functional Characterization of Porcine Adeno-Associated Viruses.
Authors: Austin Nelson / Mario Mietzsch / Jane Hsi / Julia Eby / Paul Chipman / Robert McKenna /
Abstract: Current gene therapy treatments utilizing adeno-associated virus (AAV) vectors are based on capsids of primate origin. However, pre-existing neutralizing anti-AAV antibodies, that are present in a ...Current gene therapy treatments utilizing adeno-associated virus (AAV) vectors are based on capsids of primate origin. However, pre-existing neutralizing anti-AAV antibodies, that are present in a significant portion of the population, can lead to vector inactivation and reduced therapeutic efficacy. Advances in DNA sequencing have facilitated the discovery of many AAVs from non-primate species, including isolates from pigs, which exhibit up to 50% capsid protein sequence divergence, compared to primate AAV serotypes. In this study, AAVs isolated from porcine tissues (AAVpo.1 and AAVpo.6) were selected for structural characterization due to their low capsid protein VP1 sequence identity compared to each other and to AAV9. The AAV vectors were produced via the standard triple transfection system in HEK293 cells using AAV2 to package AAV2-ITR vector genomes and were purified by iodixanol density gradient ultracentrifugation. The capsid structures of AAVpo.1 and AAVpo.6 were determined using cryo-electron microscopy and then compared to each other in addition to the AAV5 and AAV9 structures. Given that porcine AAVpo.6 has been reported to infect human cells and the ability to cross the blood-brain barrier, the functional characterization was focused on the identification of a potential glycan receptor utilized by the porcine capsids. Additionally, the porcine AAV capsid reactivity to human derived anti-AAV antibodies was assessed to evaluate the potential for these capsids to be used as alternative vectors for gene therapy, particularly for patients with pre-existing immunity to primate-derived AAV serotypes.
History
DepositionMar 14, 2025-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49739.png

Downloads & links

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Map

FileDownload / File: emd_49739.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)X (Row.)Y (Col.)
0.83 Å/pix.
x 420 pix.
= 348.6 Å		0.83 Å/pix.
x 420 pix.
= 348.6 Å		0.83 Å/pix.
x 420 pix.
= 348.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-7.620652 - 16.291378000000002
Average (Standard dev.)-0.00000000215616 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-210-210-210
Dimensions420420420
Spacing420420420
CellA=B=C: 348.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_49739_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49739_half_map_2.map
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Adeno-associated virus

EntireName: Adeno-associated virus
Components
  • Virus: Adeno-associated virus
    • Protein or peptide: Capsid protein VP1

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Supramolecule #1: Adeno-associated virus

SupramoleculeName: Adeno-associated virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 272636 / Sci species name: Adeno-associated virus / Sci species strain: AAVpo.6 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Adeno-associated virus / Strain: AAVpo.6
Molecular weightTheoretical: 59.349449 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASGSGAPMA DNNEGADGVG NASGNWHCDS TWLGDRVITT STRTWALPTY NNHLYKQISS QSGANNDNHY FGYSTPWGYF DFNRFHCHF SPRDWQRLIN NNWGFRPKRL NFKLFNIQVK EVTQTDGTKT IANNLTSTVQ VFADSEYQLP YVLGSAHQGC F PPFPADVF ...String:
MASGSGAPMA DNNEGADGVG NASGNWHCDS TWLGDRVITT STRTWALPTY NNHLYKQISS QSGANNDNHY FGYSTPWGYF DFNRFHCHF SPRDWQRLIN NNWGFRPKRL NFKLFNIQVK EVTQTDGTKT IANNLTSTVQ VFADSEYQLP YVLGSAHQGC F PPFPADVF MVPQYGYLTL NNGSQAMGRS SFYCLEYFPS QMLRTGNNFT FSYTFEDVPF HSSYAHSQSL DRLMNPLIDQ YL YYLSKTQ NGLGFSQAGH NSMRDQSRNW LPGPCFRQQR ISKTPTQNNT GDFAWTGTTR YHLNGRNSAM NPGPAMASHK DDE ERFFPQ NGVLIFGKED AEKNNAVLDK VIITDEEEIR TTNPVATGEY GLVATNFQNN TTAADTEMVN AQGILPGMVW QDRD VYLQG PIWAKIPHTD GHFHPSPLMG GFGLKRPPPQ ILIKNTPVPA DPATTFNPAK LASFITQYST GQVSVEIEWE LQKEN SKRW NPEVQYTSNY NKSVNVEFTV DNNGVYSEPR TIGTRYLTRN L

UniProtKB: Capsid protein VP1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.77 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 539729
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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