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- EMDB-41208: Avian Adeno-associated virus - empty capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-41208
TitleAvian Adeno-associated virus - empty capsid
Map data
Sample
  • Virus: Avian adeno-associated virus
    • Protein or peptide: Capsid proteinCapsid
KeywordsAdeno-associated virus / capsid / quail bronchitis / avianAAV / AAAV / 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 speciesAvian adeno-associated virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsHsi J / Mietzsch M / Chipman P / Afione S / Zeher A / Huang R / Chiorini J / McKenna R
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH GM082946 United States
CitationJournal: J Virol / Year: 2023
Title: Structural and antigenic characterization of the avian adeno-associated virus capsid.
Authors: Jane Hsi / Mario Mietzsch / Paul Chipman / Sandra Afione / Allison Zeher / Rick Huang / John Chiorini / Robert McKenna /
Abstract: AAVs are extensively studied as promising therapeutic gene delivery vectors. In order to circumvent pre-existing antibodies targeting primate-based AAV capsids, the AAAV capsid was evaluated as an ...AAVs are extensively studied as promising therapeutic gene delivery vectors. In order to circumvent pre-existing antibodies targeting primate-based AAV capsids, the AAAV capsid was evaluated as an alternative to primate-based therapeutic vectors. Despite the high sequence diversity, the AAAV capsid was found to bind to a common glycan receptor, terminal galactose, which is also utilized by other AAVs already being utilized in gene therapy trials. However, contrary to the initial hypothesis, AAAV was recognized by approximately 30% of human sera tested. Structural and sequence comparisons point to conserved epitopes in the fivefold region of the capsid as the reason determinant for the observed cross-reactivity.
History
DepositionJul 7, 2023-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateNov 8, 2023-
Current statusNov 8, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41208.png

Downloads & links

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Map

FileDownload / File: emd_41208.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.052 Å
Density
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-10.850899999999999 - 16.382587000000001
Average (Standard dev.)0.000000005105623 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-210-210-210
Dimensions420420420
Spacing420420420
CellA=B=C: 441.84003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_41208_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_41208_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 : Avian adeno-associated virus

EntireName: Avian adeno-associated virus
Components
  • Virus: Avian adeno-associated virus
    • Protein or peptide: Capsid proteinCapsid

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Supramolecule #1: Avian adeno-associated virus

SupramoleculeName: Avian adeno-associated virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 341671 / Sci species name: Avian adeno-associated virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes

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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: Avian adeno-associated virus
Molecular weightTheoretical: 60.2375 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAEGGGGPVG DAGQGADGVG NSSGNWHCDS QWLENGVVTR TTRTWVLPSY NNHLYKRIQG PSGGDNNNKF FGFSTPWGYF DYNRFHCHF SPRDWQRLIN NNWGIRPKAM RFRLFNIQVK EVTVQDSNTT IANNLTSTVQ VFADKDYQLP YVLGSATEGT F PPFPADIY ...String:
MAEGGGGPVG DAGQGADGVG NSSGNWHCDS QWLENGVVTR TTRTWVLPSY NNHLYKRIQG PSGGDNNNKF FGFSTPWGYF DYNRFHCHF SPRDWQRLIN NNWGIRPKAM RFRLFNIQVK EVTVQDSNTT IANNLTSTVQ VFADKDYQLP YVLGSATEGT F PPFPADIY TIPQYGYCTL NYNNEAVDRS AFYCLDYFPS DMLRTGNNFE FTYTFEDVPF HSMFAHNQTL DRLMNPLVDQ YL WAFSSVS QAGSSGRALH YSRATKTNMA AQYRNWLPGP FFRDQQIFTG ASNITKNNVF SVWEKGKQWE LDNRTNLMQP GPA AATTFS GEPDRQAMQN TLAFSRTVYD QTTATTDRNQ ILITNEDEIR PTNSVGIDAW GAVPTNNQSI VTPGTRAAVN NQGA LPGMV WQNRDIYLQG PIWAKIPDTD NHFHPSPLIG GFGCKHPPPQ IFIKNTPVPA NPSETFQTAK VASFINQYST GQCTV EIFW ELKKETSKRW NPEIQFTSNF GNAADIQFAV SDTGSYSEPR PIGTRYLTKP 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.4 µm
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 61.0 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: COMMON LINE
Final angle assignmentType: COMMON LINE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 38672

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