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- EMDB-76772: The AAV2 capsid in complex with IgG-Fab#3-4 -

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Basic information

Entry
Database: EMDB / ID: EMD-76772
TitleThe AAV2 capsid in complex with IgG-Fab#3-4
Map data
Sample
  • Complex: AAV2 capsid in complex with IgG-Fab3-2
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: IgG Fab3-4 heavy chain
    • Protein or peptide: IgG Fab3-4 light chain
KeywordsAAV / gene therapy / antibody / cryo-EM / IgA / Neutralization / VIRUS
Function / homology
Function and homology information


symbiont entry into host cell via permeabilization of host membrane / T=1 icosahedral viral capsid / host cell nucleolus / clathrin-dependent endocytosis of virus by host cell / virion attachment to host cell / 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 VP1/VP2 / Capsid/spike protein, ssDNA virus
Similarity search - Domain/homology
Biological speciesadeno-associated virus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsZachery J / 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: Nat Commun / Year: 2026
Title: Broadly cross-reactive anti-capsid IgA is an overlooked antibody 1 barrier in AAV2 mediated gene transfer
Authors: Logan GJ / Khandekar N / Hall B / Zachery J / Mandwie M / Hsi-Bell J / Huang A / Vyas K / Anderson D / Knight M / Farrar MA / Lisowski L / Reed JH / Mietzsch M / McKenna R / Alexander IE
History
DepositionApr 20, 2026-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76772.png

Downloads & links

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Map

FileDownload / File: emd_76772.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
0.73 Å/pix.
x 600 pix.
= 439.2 Å		0.73 Å/pix.
x 600 pix.
= 439.2 Å		0.73 Å/pix.
x 600 pix.
= 439.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.732 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-10.419957 - 16.150829999999999
Average (Standard dev.)-0.000000001921583 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-300-300-300
Dimensions600600600
Spacing600600600
CellA=B=C: 439.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_76772_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_76772_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 : AAV2 capsid in complex with IgG-Fab3-2

EntireName: AAV2 capsid in complex with IgG-Fab3-2
Components
  • Complex: AAV2 capsid in complex with IgG-Fab3-2
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: IgG Fab3-4 heavy chain
    • Protein or peptide: IgG Fab3-4 light chain

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Supramolecule #1: AAV2 capsid in complex with IgG-Fab3-2

SupramoleculeName: AAV2 capsid in complex with IgG-Fab3-2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: adeno-associated virus 2

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Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: adeno-associated virus 2
Molecular weightTheoretical: 60.120062 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MATGSGAPMA DNNEGADGVG NSSGNWHCDS TWMGDRVITT STRTWALPTY NNHLYKQISS QSGASNDNHY FGYSTPWGYF DFNRFHCHF SPRDWQRLIN NNWGFRPKRL NFKLFNIQVK EVTQNDGTTT IANNLTSTVQ VFTDSEYQLP YVLGSAHQGC L PPFPADVF ...String:
MATGSGAPMA DNNEGADGVG NSSGNWHCDS TWMGDRVITT STRTWALPTY NNHLYKQISS QSGASNDNHY FGYSTPWGYF DFNRFHCHF SPRDWQRLIN NNWGFRPKRL NFKLFNIQVK EVTQNDGTTT IANNLTSTVQ VFTDSEYQLP YVLGSAHQGC L PPFPADVF MVPQYGYLTL NNGSQAVGRS SFYCLEYFPS QMLRTGNNFT FSYTFEDVPF HSSYAHSQSL DRLMNPLIDQ YL YYLSRTN TPSGTTTQSR LQFSQAGASD IRDQSRNWLP GPCYRQQRVS KTSADNNNSE YSWTGATKYH LNGRDSLVNP GPA MASHKD DEEKFFPQSG VLIFGKQGSE KTNVDIEKVM ITDEEEIRTT NPVATEQYGS VSTNLQRGNR QAATADVNTQ GVLP GMVWQ DRDVYLQGPI WAKIPHTDGH FHPSPLMGGF GLKHPPPQIL IKNTPVPANP STTFSAAKFA SFITQYSTGQ VSVEI EWEL QKENSKRWNP EIQYTSNYNK SVNVDFTVDT NGVYSEPRPI GTRYLTRNL

UniProtKB: Capsid protein VP1

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Macromolecule #2: IgG Fab3-4 heavy chain

MacromoleculeName: IgG Fab3-4 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.022595 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VQLVESGGGV VQPGRSLRLS CAASGFTFSS YGMEWVRQAP GKGLEWVAVI WYDGSNKYYA DSVKGRFTIS RDNSKNTLYL QMNSLRAED TAVYYCARAP PQFYDTSGKA PYYYYYAMDV WGQGTT

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Macromolecule #3: IgG Fab3-4 light chain

MacromoleculeName: IgG Fab3-4 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.173064 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SVLTQPPSAS GTPGQRVTIS CSGSSSNIGS NTVNWYQQLP GTAPKLLIYS NNQRPSGVPD RFSGSRSGTS ASLAISGLQS EDEADYYCA AWDDSPNYVF GTGTKVTV

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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 GLACIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 32.44 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.45 µm / Nominal defocus min: 0.32 µm

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 22372
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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