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- EMDB-46740: Adeno-associated virus 8 capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-46740
TitleAdeno-associated virus 8 capsid
Map data
Sample
  • Virus: adeno-associated virus 8
    • Protein or peptide: Capsid protein
KeywordsParvoviridae / AAV vector / capsid / Adeno-associated virus / VIRUS
Function / homology
Function and homology information


T=1 icosahedral viral capsid / nucleotide binding / structural molecule activity
Similarity search - Function
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
Similarity search - Domain/homology
Biological speciesadeno-associated virus 8
Methodsingle particle reconstruction / cryo EM / Resolution: 2.41 Å
AuthorsMietzsch 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: Mol Ther Methods Clin Dev / Year: 2024
Title: Structural characterization and epitope mapping of the AAVX affinity purification ligand.
Authors: Mario Mietzsch / Manasi Kamat / Kari Basso / Paul Chipman / Juha T Huiskonen / Robert McKenna /
Abstract: The application of adeno-associated virus (AAV) vectors in human gene therapies requires reproducible and homogeneous preparations for clinical efficacy and safety. For the AAV production process, ...The application of adeno-associated virus (AAV) vectors in human gene therapies requires reproducible and homogeneous preparations for clinical efficacy and safety. For the AAV production process, often scalable affinity chromatography columns are utilized, such as the POROS CaptureSelect AAVX affinity resin, during downstream processing to ensure highly purified AAV vectors. The AAVX ligand is based on a camelid single-domain antibody capturing a wide range of recombinant AAV capsids. Described here is the identification of the AAV8 capsid epitope to AAVX at 2.3 Å resolution using cryo-electron microscopy. The ligand binds near the 5-fold axis of the capsid in a similar manner to the previously characterized AVB affinity ligand but does not conform to the capsid's icosahedral symmetry. The cross-reactivity of AAVX to other AAV capsids is achieved by primarily interacting with the peptide backbone of the AAV capsid's structurally conserved DE and HI loops. These observations will guide AAV capsid engineering efforts to retain the ability of future recombinant capsid designs to be purified using antibody-based affinity ligands.
History
DepositionAug 25, 2024-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46740.png

Downloads & links

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Map

FileDownload / File: emd_46740.map.gz / Format: CCP4 / Size: 634.7 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.)
0.84 Å/pix.
x 550 pix.
= 462. Å		0.84 Å/pix.
x 550 pix.
= 462. Å		0.84 Å/pix.
x 550 pix.
= 462. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-10.853376000000001 - 21.088941999999999
Average (Standard dev.)0.000000001351456 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-275-275-275
Dimensions550550550
Spacing550550550
CellA=B=C: 462.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_46740_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_46740_half_map_2.map
Projections & Slices
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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 protein

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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: SEROTYPE / Virus enveloped: No / Virus empty: No
Virus shellShell ID: 1 / T number (triangulation number): 1

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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: 59.943891 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAGGGAPMA DNNEGADGVG SSSGNWHCDS TWLGDRVITT STRTWALPTY NNHLYKQISN GTSGGATNDN TYFGYSTPWG YFDFNRFHC HFSPRDWQRL INNNWGFRPK RLSFKLFNIQ VKEVTQNEGT KTIANNLTST IQVFTDSEYQ LPYVLGSAHQ G CLPPFPAD ...String:
MAAGGGAPMA DNNEGADGVG SSSGNWHCDS TWLGDRVITT STRTWALPTY NNHLYKQISN GTSGGATNDN TYFGYSTPWG YFDFNRFHC HFSPRDWQRL INNNWGFRPK RLSFKLFNIQ VKEVTQNEGT KTIANNLTST IQVFTDSEYQ LPYVLGSAHQ G CLPPFPAD VFMIPQYGYL TLNNGSQAVG RSSFYCLEYF PSQMLRTGNN FQFTYTFEDV PFHSSYAHSQ SLDRLMNPLI DQ YLYYLSR TQTTGGTANT QTLGFSQGGP NTMANQAKNW LPGPCYRQQR VSTTTGQNNN SNFAWTAGTK YHLNGRNSLA NPG IAMATH KDDEERFFPS NGILIFGKQN AARDNADYSD VMLTSEEEIK TTNPVATEEY GIVADNLQQQ NTAPQIGTVN SQGA LPGMV WQNRDVYLQG PIWAKIPHTD GNFHPSPLMG GFGLKHPPPQ ILIKNTPVPA DPPTTFNQSK LNSFITQYST GQVSV EIEW ELQKENSKRW NPEIQYTSNY YKSTSVDFAV NTEGVYSEPR PIGTRYLTRN L

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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (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: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.41 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 205344
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: PROJECTION MATCHING

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