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- EMDB-44273: Fab1-3 in complex with the capsid of Adeno-associated virus type 9 -

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Basic information

Entry
Database: EMDB / ID: EMD-44273
TitleFab1-3 in complex with the capsid of Adeno-associated virus type 9
Map data
Sample
  • Virus: Adeno-associated virus
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Fab1-3 heavy chain
    • Protein or peptide: Fab1-3 light chain
KeywordsAdeno-associated virus / AAV / capsid / Fab-complex / antibody / NAb / VIRUS / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.13 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: Nat Commun / Year: 2025
Title: Structural characterization of antibody-responses from Zolgensma treatment guides the design of a capsid suitable for redosing
Authors: Mietzsch M / Nelson AR / Hsi J / Zachary J / Potts L / Chipman P / Ghanem M / Alexander IE / Logan GJ / Huiskonen J / McKenna R
History
DepositionMar 25, 2024-
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_44273.png

Downloads & links

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Map

FileDownload / File: emd_44273.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
0.84 Å/pix.
x 200 pix.
= 168. Å		0.84 Å/pix.
x 200 pix.
= 168. Å		0.84 Å/pix.
x 200 pix.
= 168. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-7.641454 - 12.597329
Average (Standard dev.)0.000000006639132 (±1.0000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-100-100-100
Dimensions200200200
Spacing200200200
CellA=B=C: 168.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_44273_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_44273_half_map_2.map
Projections & Slices
AxesZYX

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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: Capsid protein VP1
    • Protein or peptide: Fab1-3 heavy chain
    • Protein or peptide: Fab1-3 light chain

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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 / 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 VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Adeno-associated virus / Strain: AAV9
Molecular weightTheoretical: 59.873875 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASGGGAPVA DNNEGADGVG SSSGNWHCDS QWLGDRVITT STRTWALPTY NNHLYKQISN STSGGSSNDN AYFGYSTPWG YFDFNRFHC HFSPRDWQRL INNNWGFRPK RLNFKLFNIQ VKEVTDNNGV KTIANNLTST VQVFTDSDYQ LPYVLGSAHE G CLPPFPAD ...String:
MASGGGAPVA DNNEGADGVG SSSGNWHCDS QWLGDRVITT STRTWALPTY NNHLYKQISN STSGGSSNDN AYFGYSTPWG YFDFNRFHC HFSPRDWQRL INNNWGFRPK RLNFKLFNIQ VKEVTDNNGV KTIANNLTST VQVFTDSDYQ LPYVLGSAHE G CLPPFPAD VFMIPQYGYL TLNDGSQAVG RSSFYCLEYF PSQMLRTGNN FQFSYEFENV PFHSSYAHSQ SLDRLMNPLI DQ YLYYLSK TINGSGQNQQ TLKFSVAGPS NMAVQGRNYI PGPSYRQQRV STTVTQNNNS EFAWPGASSW ALNGRNSLMN PGP AMASHK EGEDRFFPLS GSLIFGKQGT GRDNVDADKV MITNEEEIKT TNPVATESYG QVATNHQSAQ AQAQTGWVQN QGIL PGMVW QDRDVYLQGP IWAKIPHTDG NFHPSPLMGG FGMKHPPPQI LIKNTPVPAD PPTAFNKDKL NSFITQYSTG QVSVE IEWE LQKENSKRWN PEIQYTSNYY KSNNVEFAVN TEGVYSEPRP IGTRYLTRNL

UniProtKB: Capsid protein VP1

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Macromolecule #2: Fab1-3 heavy chain

MacromoleculeName: Fab1-3 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.089645 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VQLVESGGGV VQPGRSLRLS CAASGFSFSS FVFHWVRQAP GKGLEWVAVI SYDGSNKNYA DSVKGRFTIS RDNSKNTLFL QMNSLSADD TAVYYCARGA ICSSTTCYLG DSYYFYGMDV WGQGTTVTVS S

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Macromolecule #3: Fab1-3 light chain

MacromoleculeName: Fab1-3 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.244273 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
LTQPPSVSGA PGQRVTISCT GSRSNIGAGY DVHWYQQLPG TAPKLLIYGN SNRPSGVPDR FSGSKSGTSA SLAITGLQTD DEADYYCQS YDSSLSGSVF GGGTKLTVLG

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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: 2.1 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: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 410892
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: PROJECTION MATCHING

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