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- EMDB-36594: Cryo-EM structure of a designed AAV8-based vector -

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Basic information

Entry
Database: EMDB / ID: EMD-36594
TitleCryo-EM structure of a designed AAV8-based vector
Map data
Sample
  • Virus: Adeno-associated virus - 8
    • Protein or peptide: Capsid proteinCapsid
KeywordsAAV8 / 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
Function and homology information
Biological speciesAdeno-associated virus - 8
Methodsingle particle reconstruction / cryo EM / Resolution: 2.08 Å
AuthorsKe X / Luo S / Zheng Q / Jiang H / Liu F / Sun X
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: An adeno-associated virus variant enabling efficient ocular-directed gene delivery across species.
Authors: Shuang Luo / Hao Jiang / Qingwei Li / Yingfei Qin / Shiping Yang / Jing Li / Lingli Xu / Yan Gou / Yafei Zhang / Fengjiang Liu / Xiao Ke / Qiang Zheng / Xun Sun /
Abstract: Recombinant adeno-associated viruses (rAAVs) have emerged as promising gene therapy vectors due to their proven efficacy and safety in clinical applications. In non-human primates (NHPs), rAAVs are ...Recombinant adeno-associated viruses (rAAVs) have emerged as promising gene therapy vectors due to their proven efficacy and safety in clinical applications. In non-human primates (NHPs), rAAVs are administered via suprachoroidal injection at a higher dose. However, high doses of rAAVs tend to increase additional safety risks. Here, we present a novel AAV capsid (AAVv128), which exhibits significantly enhanced transduction efficiency for photoreceptors and retinal pigment epithelial (RPE) cells, along with a broader distribution across the layers of retinal tissues in different animal models (mice, rabbits, and NHPs) following intraocular injection. Notably, the suprachoroidal delivery of AAVv128-anti-VEGF vector completely suppresses the Grade IV lesions in a laser-induced choroidal neovascularization (CNV) NHP model for neovascular age-related macular degeneration (nAMD). Furthermore, cryo-EM analysis at 2.1 Å resolution reveals that the critical residues of AAVv128 exhibit a more robust advantage in AAV binding, the nuclear uptake and endosome escaping. Collectively, our findings highlight the potential of AAVv128 as a next generation ocular gene therapy vector, particularly using the suprachoroidal delivery route.
History
DepositionJun 16, 2023-
Header (metadata) releaseApr 24, 2024-
Map releaseApr 24, 2024-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36594.png

Downloads & links

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Map

FileDownload / File: emd_36594.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.73 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.3326438 - 0.759319
Average (Standard dev.)0.0016344875 (±0.06158229)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 327.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36594_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36594_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Adeno-associated virus - 8

EntireName: Adeno-associated virus - 8
Components
  • Virus: Adeno-associated virus - 8
    • Protein or peptide: Capsid proteinCapsid

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Supramolecule #1: Adeno-associated virus - 8

SupramoleculeName: Adeno-associated virus - 8 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 202813 / Sci species name: Adeno-associated virus - 8 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Adeno-associated virus - 8
Molecular weightTheoretical: 59.270191 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GADGVGSSSG NWHCDSTWLG DRVITTSTRT WALPTYNNHL YKQISNGTSG GATNDNTYFG YSTPWGYFDF NRFHCHFSPR DWQRLINNN WGFRPKRLSF KLFNIQVKEV TQNEGTKTIA NNLTSTIQVF TDSEYQLPYV LGSAHQGCLP PFPADVFMIP Q YGYLTLNN ...String:
GADGVGSSSG NWHCDSTWLG DRVITTSTRT WALPTYNNHL YKQISNGTSG GATNDNTYFG YSTPWGYFDF NRFHCHFSPR DWQRLINNN WGFRPKRLSF KLFNIQVKEV TQNEGTKTIA NNLTSTIQVF TDSEYQLPYV LGSAHQGCLP PFPADVFMIP Q YGYLTLNN GSQAVGRSSF YCLEYFPSQM LRTGNNFQFT YTFEDVPFHS SYAHSQSLDR LMNPLIDQYL YYLSRTQTTG GT ANTQTLG FSQGGPNTMA NQAKNWLPGP CYRQQRVSTT TGQNNNSNFA WTAGTKYHLN GRNSLANPGI AMATHKDDEE RFF PSNGIL IFGKQNAARD NADYSDVMLT SEEEIKTTNP VATEEYGIVA DNLQRGNQQN TARQPQIGTV NSQGALPGMV WQNR DVYLQ GPIWAKIPHT DGNFHPSPLM GGFGLKHPPP QILIKNTPVP ADPPTTFNQS KLNSFITQYS TGQVSVEIEW ELQKE NSKR WNPEIQYTSN YYKSTSVDFA VNTEGVYSEP RPIGTRYLTR NL

UniProtKB: Capsid protein

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 90744

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