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- PDB-12ut: The AAV2 capsid in complex with IgA-Fab#3-2 -

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Basic information

Entry
Database: PDB / ID: 12ut
TitleThe AAV2 capsid in complex with IgA-Fab#3-2
Components
  • Capsid protein VP1
  • IgA-Fab3-2 Heavy chain
  • IgA-Fab3-2 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: 2.48 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
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
0: 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
7: Capsid protein VP1
Ah: IgA-Fab3-2 Heavy chain
Bh: IgA-Fab3-2 Heavy chain
Ch: IgA-Fab3-2 Heavy chain
Dh: IgA-Fab3-2 Heavy chain
Eh: IgA-Fab3-2 Heavy chain
Fh: IgA-Fab3-2 Heavy chain
Gh: IgA-Fab3-2 Heavy chain
Hh: IgA-Fab3-2 Heavy chain
Ih: IgA-Fab3-2 Heavy chain
Jh: IgA-Fab3-2 Heavy chain
Kh: IgA-Fab3-2 Heavy chain
Lh: IgA-Fab3-2 Heavy chain
Mh: IgA-Fab3-2 Heavy chain
Nh: IgA-Fab3-2 Heavy chain
Oh: IgA-Fab3-2 Heavy chain
Ph: IgA-Fab3-2 Heavy chain
Qh: IgA-Fab3-2 Heavy chain
Rh: IgA-Fab3-2 Heavy chain
Sh: IgA-Fab3-2 Heavy chain
Th: IgA-Fab3-2 Heavy chain
Uh: IgA-Fab3-2 Heavy chain
Vh: IgA-Fab3-2 Heavy chain
Wh: IgA-Fab3-2 Heavy chain
Xh: IgA-Fab3-2 Heavy chain
Yh: IgA-Fab3-2 Heavy chain
Zh: IgA-Fab3-2 Heavy chain
ah: IgA-Fab3-2 Heavy chain
bh: IgA-Fab3-2 Heavy chain
ch: IgA-Fab3-2 Heavy chain
dh: IgA-Fab3-2 Heavy chain
eh: IgA-Fab3-2 Heavy chain
fh: IgA-Fab3-2 Heavy chain
gh: IgA-Fab3-2 Heavy chain
hh: IgA-Fab3-2 Heavy chain
ih: IgA-Fab3-2 Heavy chain
jh: IgA-Fab3-2 Heavy chain
kh: IgA-Fab3-2 Heavy chain
lh: IgA-Fab3-2 Heavy chain
mh: IgA-Fab3-2 Heavy chain
nh: IgA-Fab3-2 Heavy chain
oh: IgA-Fab3-2 Heavy chain
ph: IgA-Fab3-2 Heavy chain
qh: IgA-Fab3-2 Heavy chain
rh: IgA-Fab3-2 Heavy chain
sh: IgA-Fab3-2 Heavy chain
th: IgA-Fab3-2 Heavy chain
uh: IgA-Fab3-2 Heavy chain
vh: IgA-Fab3-2 Heavy chain
wh: IgA-Fab3-2 Heavy chain
xh: IgA-Fab3-2 Heavy chain
yh: IgA-Fab3-2 Heavy chain
zh: IgA-Fab3-2 Heavy chain
0h: IgA-Fab3-2 Heavy chain
1h: IgA-Fab3-2 Heavy chain
2h: IgA-Fab3-2 Heavy chain
3h: IgA-Fab3-2 Heavy chain
4h: IgA-Fab3-2 Heavy chain
5h: IgA-Fab3-2 Heavy chain
6h: IgA-Fab3-2 Heavy chain
7h: IgA-Fab3-2 Heavy chain
Al: IgA-Fab3-2 Light chain
Bl: IgA-Fab3-2 Light chain
Cl: IgA-Fab3-2 Light chain
Dl: IgA-Fab3-2 Light chain
El: IgA-Fab3-2 Light chain
Fl: IgA-Fab3-2 Light chain
Gl: IgA-Fab3-2 Light chain
Hl: IgA-Fab3-2 Light chain
Il: IgA-Fab3-2 Light chain
Jl: IgA-Fab3-2 Light chain
Kl: IgA-Fab3-2 Light chain
Ll: IgA-Fab3-2 Light chain
Ml: IgA-Fab3-2 Light chain
Nl: IgA-Fab3-2 Light chain
Ol: IgA-Fab3-2 Light chain
Pl: IgA-Fab3-2 Light chain
Ql: IgA-Fab3-2 Light chain
Rl: IgA-Fab3-2 Light chain
Sl: IgA-Fab3-2 Light chain
Tl: IgA-Fab3-2 Light chain
Ul: IgA-Fab3-2 Light chain
Vl: IgA-Fab3-2 Light chain
Wl: IgA-Fab3-2 Light chain
Xl: IgA-Fab3-2 Light chain
Yl: IgA-Fab3-2 Light chain
Zl: IgA-Fab3-2 Light chain
al: IgA-Fab3-2 Light chain
bl: IgA-Fab3-2 Light chain
cl: IgA-Fab3-2 Light chain
dl: IgA-Fab3-2 Light chain
el: IgA-Fab3-2 Light chain
fl: IgA-Fab3-2 Light chain
gl: IgA-Fab3-2 Light chain
hl: IgA-Fab3-2 Light chain
il: IgA-Fab3-2 Light chain
jl: IgA-Fab3-2 Light chain
kl: IgA-Fab3-2 Light chain
ll: IgA-Fab3-2 Light chain
ml: IgA-Fab3-2 Light chain
nl: IgA-Fab3-2 Light chain
ol: IgA-Fab3-2 Light chain
pl: IgA-Fab3-2 Light chain
ql: IgA-Fab3-2 Light chain
rl: IgA-Fab3-2 Light chain
sl: IgA-Fab3-2 Light chain
tl: IgA-Fab3-2 Light chain
ul: IgA-Fab3-2 Light chain
vl: IgA-Fab3-2 Light chain
wl: IgA-Fab3-2 Light chain
xl: IgA-Fab3-2 Light chain
yl: IgA-Fab3-2 Light chain
zl: IgA-Fab3-2 Light chain
0l: IgA-Fab3-2 Light chain
1l: IgA-Fab3-2 Light chain
2l: IgA-Fab3-2 Light chain
3l: IgA-Fab3-2 Light chain
4l: IgA-Fab3-2 Light chain
5l: IgA-Fab3-2 Light chain
6l: IgA-Fab3-2 Light chain
7l: IgA-Fab3-2 Light chain


Theoretical massNumber of molelcules
Total (without water)5,448,800180
Polymers5,448,800180
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 ...
IgA-Fab3-2 Heavy chain


Mass: 16923.871 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody ...
IgA-Fab3-2 Light chain


Mass: 13769.394 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster)
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 IgA-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: 2.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10214 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01370620
ELECTRON MICROSCOPYf_angle_d0.978505080
ELECTRON MICROSCOPYf_dihedral_angle_d10.369293280
ELECTRON MICROSCOPYf_chiral_restr0.06353580
ELECTRON MICROSCOPYf_plane_restr0.00866000

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