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- PDB-12uu: The AAV2 capsid in complex with IgG-Fab#3-4 -

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Basic information

Entry
Database: PDB / ID: 12uu
TitleThe AAV2 capsid in complex with IgG-Fab#3-4
Components
  • Capsid protein VP1
  • IgG Fab3-4 heavy chain
  • IgG Fab3-4 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: 2.91 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: IgG Fab3-4 heavy chain
Bh: IgG Fab3-4 heavy chain
Ch: IgG Fab3-4 heavy chain
Dh: IgG Fab3-4 heavy chain
Eh: IgG Fab3-4 heavy chain
Fh: IgG Fab3-4 heavy chain
Gh: IgG Fab3-4 heavy chain
Hh: IgG Fab3-4 heavy chain
Ih: IgG Fab3-4 heavy chain
Jh: IgG Fab3-4 heavy chain
Kh: IgG Fab3-4 heavy chain
Lh: IgG Fab3-4 heavy chain
Mh: IgG Fab3-4 heavy chain
Nh: IgG Fab3-4 heavy chain
Oh: IgG Fab3-4 heavy chain
Ph: IgG Fab3-4 heavy chain
Qh: IgG Fab3-4 heavy chain
Rh: IgG Fab3-4 heavy chain
Sh: IgG Fab3-4 heavy chain
Th: IgG Fab3-4 heavy chain
Uh: IgG Fab3-4 heavy chain
Vh: IgG Fab3-4 heavy chain
Wh: IgG Fab3-4 heavy chain
Xh: IgG Fab3-4 heavy chain
Yh: IgG Fab3-4 heavy chain
Zh: IgG Fab3-4 heavy chain
1h: IgG Fab3-4 heavy chain
2h: IgG Fab3-4 heavy chain
3h: IgG Fab3-4 heavy chain
4h: IgG Fab3-4 heavy chain
5h: IgG Fab3-4 heavy chain
6h: IgG Fab3-4 heavy chain
ah: IgG Fab3-4 heavy chain
bh: IgG Fab3-4 heavy chain
ch: IgG Fab3-4 heavy chain
dh: IgG Fab3-4 heavy chain
eh: IgG Fab3-4 heavy chain
fh: IgG Fab3-4 heavy chain
gh: IgG Fab3-4 heavy chain
hh: IgG Fab3-4 heavy chain
ih: IgG Fab3-4 heavy chain
jh: IgG Fab3-4 heavy chain
kh: IgG Fab3-4 heavy chain
lh: IgG Fab3-4 heavy chain
mh: IgG Fab3-4 heavy chain
nh: IgG Fab3-4 heavy chain
oh: IgG Fab3-4 heavy chain
ph: IgG Fab3-4 heavy chain
qh: IgG Fab3-4 heavy chain
rh: IgG Fab3-4 heavy chain
sh: IgG Fab3-4 heavy chain
th: IgG Fab3-4 heavy chain
uh: IgG Fab3-4 heavy chain
vh: IgG Fab3-4 heavy chain
wh: IgG Fab3-4 heavy chain
xh: IgG Fab3-4 heavy chain
yh: IgG Fab3-4 heavy chain
zh: IgG Fab3-4 heavy chain
7h: IgG Fab3-4 heavy chain
8h: IgG Fab3-4 heavy chain
Al: IgG Fab3-4 light chain
Bl: IgG Fab3-4 light chain
Cl: IgG Fab3-4 light chain
Dl: IgG Fab3-4 light chain
El: IgG Fab3-4 light chain
Fl: IgG Fab3-4 light chain
Gl: IgG Fab3-4 light chain
Hl: IgG Fab3-4 light chain
Il: IgG Fab3-4 light chain
Jl: IgG Fab3-4 light chain
Kl: IgG Fab3-4 light chain
Ll: IgG Fab3-4 light chain
Ml: IgG Fab3-4 light chain
Nl: IgG Fab3-4 light chain
Ol: IgG Fab3-4 light chain
Pl: IgG Fab3-4 light chain
Ql: IgG Fab3-4 light chain
Rl: IgG Fab3-4 light chain
Sl: IgG Fab3-4 light chain
Tl: IgG Fab3-4 light chain
Ul: IgG Fab3-4 light chain
Vl: IgG Fab3-4 light chain
Wl: IgG Fab3-4 light chain
Xl: IgG Fab3-4 light chain
Yl: IgG Fab3-4 light chain
Zl: IgG Fab3-4 light chain
1l: IgG Fab3-4 light chain
2l: IgG Fab3-4 light chain
3l: IgG Fab3-4 light chain
4l: IgG Fab3-4 light chain
5l: IgG Fab3-4 light chain
6l: IgG Fab3-4 light chain
al: IgG Fab3-4 light chain
bl: IgG Fab3-4 light chain
cl: IgG Fab3-4 light chain
dl: IgG Fab3-4 light chain
el: IgG Fab3-4 light chain
fl: IgG Fab3-4 light chain
gl: IgG Fab3-4 light chain
hl: IgG Fab3-4 light chain
il: IgG Fab3-4 light chain
jl: IgG Fab3-4 light chain
kl: IgG Fab3-4 light chain
ll: IgG Fab3-4 light chain
ml: IgG Fab3-4 light chain
nl: IgG Fab3-4 light chain
ol: IgG Fab3-4 light chain
pl: IgG Fab3-4 light chain
ql: IgG Fab3-4 light chain
rl: IgG Fab3-4 light chain
sl: IgG Fab3-4 light chain
tl: IgG Fab3-4 light chain
ul: IgG Fab3-4 light chain
vl: IgG Fab3-4 light chain
wl: IgG Fab3-4 light chain
xl: IgG Fab3-4 light chain
yl: IgG Fab3-4 light chain
zl: IgG Fab3-4 light chain
7l: IgG Fab3-4 light chain
8l: IgG Fab3-4 light chain


Theoretical massNumber of molelcules
Total (without water)5,118,943180
Polymers5,118,943180
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 ...
IgG Fab3-4 heavy chain


Mass: 14022.595 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 ...
IgG Fab3-4 light chain


Mass: 11173.064 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
5cryoSPARCCTF correction
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22372 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.015362580
ELECTRON MICROSCOPYf_angle_d1.121494340
ELECTRON MICROSCOPYf_dihedral_angle_d10.374287280
ELECTRON MICROSCOPYf_chiral_restr0.07451480
ELECTRON MICROSCOPYf_plane_restr0.00965160

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