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- EMDB-49042: The capsid structure of AAVpo.1 -

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Basic information

Entry
Database: EMDB / ID: EMD-49042
TitleThe capsid structure of AAVpo.1
Map data
Sample
  • Virus: Adeno-associated virus
    • Protein or peptide: VP3
KeywordsAAVpo.1 / porcine adeno-associated virus / gene therapy / vector / cryo-EM / VIRUS
Function / homologyParvovirus 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 / VP3
Function and homology information
Biological speciesAdeno-associated virus - Po1 / Adeno-associated virus
Methodsingle particle reconstruction / cryo EM / Resolution: 1.79 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: To Be Published
Title: Structural insights into porcine adeno-associated viruses
Authors: Nelson A / Mietzsch M / Eby J / Chipman P / McKenna R
History
DepositionFeb 4, 2025-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49042.png

Downloads & links

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Map

FileDownload / File: emd_49042.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-7.2216706 - 15.571158
Average (Standard dev.)0.000000003361142 (±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: #2

Fileemd_49042_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_49042_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

EntireName: Adeno-associated virus
Components
  • Virus: Adeno-associated virus
    • Protein or peptide: VP3

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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.1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Macromolecule #1: VP3

MacromoleculeName: VP3 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Adeno-associated virus - Po1 / Strain: AAVpo.1
Molecular weightTheoretical: 60.185117 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSAGGGSPLG DNNQGADGVG NASGDWHCDS TWMGDRVITK STRTWVLPSY NNHQYLEIHS GSVDGSNANA YFGYSTPWGY FDFNRFHSH WSPRDWQRLV NNYWGFRPRS LKVKIFNIQV KEVTTQDGTT TIANNLTSTV QVFTDNDYQL PYVIGNGTEG C LPAFPPQV ...String:
MSAGGGSPLG DNNQGADGVG NASGDWHCDS TWMGDRVITK STRTWVLPSY NNHQYLEIHS GSVDGSNANA YFGYSTPWGY FDFNRFHSH WSPRDWQRLV NNYWGFRPRS LKVKIFNIQV KEVTTQDGTT TIANNLTSTV QVFTDNDYQL PYVIGNGTEG C LPAFPPQV FTLPQYGYAT LNRNNTDDPT ERSSFFCLEY FPSKMLRTGN NFEFTYSFEE VPFHCSFAPS QNLFKLANPL VD QYLYRFV STDTSGNLQF QKNLKARYAN TYKNWFPGPM CRTQGWYTSA GTYNNKGVAN FDTSNKMELE GASYQVNPQP NGM TNTLQD SNKYALENTM IFNAQNAPPG TTSLYQENNL LITSESETQP VNRLAYNTGG QVSNNNQNSN THPTVGVYNH QEVL PGSVW MDRDVYLQGP IWAKIPETGA HFHPSPAMGG FGLKHPPPMM LIKNTPVPSN VAAFSDVPVK SFITQYSTGQ VTVEI EWEL KKENSKRWNP EIQYTNNYNN PTFVDFAPDT SGEYRTTRAI GTRYLTRPL

UniProtKB: VP3

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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

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.79 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 512823
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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