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- PDB-12us: The AAV2 capsid in complex with IgG-Fab#3-2 -

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Basic information

Entry
Database: PDB / ID: 12us
TitleThe AAV2 capsid in complex with IgG-Fab#3-2
Components
  • Capsid protein VP1
  • Fab3-2 IgG Heavy chain
  • Fab3-2 IgG Light Chain
KeywordsVIRUS / AAV / gene therapy / antibody / cryo-EM / IgA / Neutralization
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsZachery, J. / Mietzsch, M. / McKenna, R.
Funding support United States, 1items
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, G.J. / Khandekar, N. / Hall, B. / Zachery, J. / Mandwie, M. / Hsi-Bell, J. / Huang, A. / Vyas, K. / Anderson, D. / Knight, M. / Farrar, M.A. / Lisowski, L. / Reed, J.H. / Mietzsch, M. ...Authors: Logan, G.J. / Khandekar, N. / Hall, B. / Zachery, J. / Mandwie, M. / Hsi-Bell, J. / Huang, A. / Vyas, K. / Anderson, D. / Knight, M. / Farrar, M.A. / Lisowski, L. / Reed, J.H. / Mietzsch, M. / McKenna, R. / Alexander, I.E.
History
DepositionApr 20, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein VP1
B: Capsid protein VP1
C: Capsid protein VP1
D: Capsid protein VP1
E: Capsid protein VP1
F: Capsid protein VP1
G: Capsid protein VP1
H: Capsid protein VP1
I: Capsid protein VP1
J: Capsid protein VP1
K: Capsid protein VP1
L: Capsid protein VP1
M: Capsid protein VP1
N: Capsid protein VP1
O: Capsid protein VP1
P: Capsid protein VP1
Q: Capsid protein VP1
R: Capsid protein VP1
S: Capsid protein VP1
T: Capsid protein VP1
U: Capsid protein VP1
V: Capsid protein VP1
W: Capsid protein VP1
X: Capsid protein VP1
Y: Capsid protein VP1
Z: Capsid protein VP1
1: Capsid protein VP1
2: Capsid protein VP1
3: Capsid protein VP1
4: Capsid protein VP1
5: Capsid protein VP1
6: Capsid protein VP1
a: Capsid protein VP1
b: Capsid protein VP1
c: Capsid protein VP1
d: Capsid protein VP1
e: Capsid protein VP1
f: Capsid protein VP1
g: Capsid protein VP1
h: Capsid protein VP1
i: Capsid protein VP1
j: Capsid protein VP1
k: Capsid protein VP1
l: Capsid protein VP1
m: Capsid protein VP1
n: Capsid protein VP1
o: Capsid protein VP1
p: Capsid protein VP1
q: Capsid protein VP1
r: Capsid protein VP1
s: Capsid protein VP1
t: Capsid protein VP1
u: Capsid protein VP1
v: Capsid protein VP1
w: Capsid protein VP1
x: Capsid protein VP1
y: Capsid protein VP1
z: Capsid protein VP1
7: Capsid protein VP1
8: Capsid protein VP1
Ah: Fab3-2 IgG Heavy chain
Bh: Fab3-2 IgG Heavy chain
Ch: Fab3-2 IgG Heavy chain
Dh: Fab3-2 IgG Heavy chain
Eh: Fab3-2 IgG Heavy chain
Fh: Fab3-2 IgG Heavy chain
Gh: Fab3-2 IgG Heavy chain
Hh: Fab3-2 IgG Heavy chain
Ih: Fab3-2 IgG Heavy chain
Jh: Fab3-2 IgG Heavy chain
Kh: Fab3-2 IgG Heavy chain
Lh: Fab3-2 IgG Heavy chain
Mh: Fab3-2 IgG Heavy chain
Nh: Fab3-2 IgG Heavy chain
Oh: Fab3-2 IgG Heavy chain
Ph: Fab3-2 IgG Heavy chain
Qh: Fab3-2 IgG Heavy chain
Rh: Fab3-2 IgG Heavy chain
Sh: Fab3-2 IgG Heavy chain
Th: Fab3-2 IgG Heavy chain
Uh: Fab3-2 IgG Heavy chain
Vh: Fab3-2 IgG Heavy chain
Wh: Fab3-2 IgG Heavy chain
Xh: Fab3-2 IgG Heavy chain
Yh: Fab3-2 IgG Heavy chain
Zh: Fab3-2 IgG Heavy chain
1h: Fab3-2 IgG Heavy chain
2h: Fab3-2 IgG Heavy chain
3h: Fab3-2 IgG Heavy chain
4h: Fab3-2 IgG Heavy chain
5h: Fab3-2 IgG Heavy chain
6h: Fab3-2 IgG Heavy chain
ah: Fab3-2 IgG Heavy chain
bh: Fab3-2 IgG Heavy chain
ch: Fab3-2 IgG Heavy chain
dh: Fab3-2 IgG Heavy chain
eh: Fab3-2 IgG Heavy chain
fh: Fab3-2 IgG Heavy chain
gh: Fab3-2 IgG Heavy chain
hh: Fab3-2 IgG Heavy chain
ih: Fab3-2 IgG Heavy chain
jh: Fab3-2 IgG Heavy chain
kh: Fab3-2 IgG Heavy chain
lh: Fab3-2 IgG Heavy chain
mh: Fab3-2 IgG Heavy chain
nh: Fab3-2 IgG Heavy chain
oh: Fab3-2 IgG Heavy chain
ph: Fab3-2 IgG Heavy chain
qh: Fab3-2 IgG Heavy chain
rh: Fab3-2 IgG Heavy chain
sh: Fab3-2 IgG Heavy chain
th: Fab3-2 IgG Heavy chain
uh: Fab3-2 IgG Heavy chain
vh: Fab3-2 IgG Heavy chain
wh: Fab3-2 IgG Heavy chain
xh: Fab3-2 IgG Heavy chain
yh: Fab3-2 IgG Heavy chain
zh: Fab3-2 IgG Heavy chain
7h: Fab3-2 IgG Heavy chain
8h: Fab3-2 IgG Heavy chain
Al: Fab3-2 IgG Light Chain
Bl: Fab3-2 IgG Light Chain
Cl: Fab3-2 IgG Light Chain
Dl: Fab3-2 IgG Light Chain
El: Fab3-2 IgG Light Chain
Fl: Fab3-2 IgG Light Chain
Gl: Fab3-2 IgG Light Chain
Hl: Fab3-2 IgG Light Chain
Il: Fab3-2 IgG Light Chain
Jl: Fab3-2 IgG Light Chain
Kl: Fab3-2 IgG Light Chain
Ll: Fab3-2 IgG Light Chain
Ml: Fab3-2 IgG Light Chain
Nl: Fab3-2 IgG Light Chain
Ol: Fab3-2 IgG Light Chain
Pl: Fab3-2 IgG Light Chain
Ql: Fab3-2 IgG Light Chain
Rl: Fab3-2 IgG Light Chain
Sl: Fab3-2 IgG Light Chain
Tl: Fab3-2 IgG Light Chain
Ul: Fab3-2 IgG Light Chain
Vl: Fab3-2 IgG Light Chain
Wl: Fab3-2 IgG Light Chain
Xl: Fab3-2 IgG Light Chain
Yl: Fab3-2 IgG Light Chain
Zl: Fab3-2 IgG Light Chain
1l: Fab3-2 IgG Light Chain
2l: Fab3-2 IgG Light Chain
3l: Fab3-2 IgG Light Chain
4l: Fab3-2 IgG Light Chain
5l: Fab3-2 IgG Light Chain
6l: Fab3-2 IgG Light Chain
al: Fab3-2 IgG Light Chain
bl: Fab3-2 IgG Light Chain
cl: Fab3-2 IgG Light Chain
dl: Fab3-2 IgG Light Chain
el: Fab3-2 IgG Light Chain
fl: Fab3-2 IgG Light Chain
gl: Fab3-2 IgG Light Chain
hl: Fab3-2 IgG Light Chain
il: Fab3-2 IgG Light Chain
jl: Fab3-2 IgG Light Chain
kl: Fab3-2 IgG Light Chain
ll: Fab3-2 IgG Light Chain
ml: Fab3-2 IgG Light Chain
nl: Fab3-2 IgG Light Chain
ol: Fab3-2 IgG Light Chain
pl: Fab3-2 IgG Light Chain
ql: Fab3-2 IgG Light Chain
rl: Fab3-2 IgG Light Chain
sl: Fab3-2 IgG Light Chain
tl: Fab3-2 IgG Light Chain
ul: Fab3-2 IgG Light Chain
vl: Fab3-2 IgG Light Chain
wl: Fab3-2 IgG Light Chain
xl: Fab3-2 IgG Light Chain
yl: Fab3-2 IgG Light Chain
zl: Fab3-2 IgG Light Chain
7l: Fab3-2 IgG Light Chain
8l: Fab3-2 IgG Light Chain


Theoretical massNumber of molelcules
Total (without water)5,168,213180
Polymers5,168,213180
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
Capsid protein VP1


Mass: 60120.062 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) adeno-associated virus 2 / Gene: VP1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P03135
#2: Antibody ...
Fab3-2 IgG Heavy chain


Mass: 14540.171 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Antibody ...
Fab3-2 IgG Light Chain


Mass: 11476.655 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: AAV2 capsid in complex with IgG-Fab3-2 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: adeno-associated virus 2
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2450 nm / Nominal defocus min: 320 nm
Image recordingElectron dose: 32.44 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.10-2155_2155model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35713 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01370260
ELECTRON MICROSCOPYf_angle_d0.86504600
ELECTRON MICROSCOPYf_dihedral_angle_d10.185292980
ELECTRON MICROSCOPYf_chiral_restr0.05653520
ELECTRON MICROSCOPYf_plane_restr0.00665940

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