12US | pdb_000012us

The AAV2 capsid in complex with IgG-Fab#3-2

• PDB DOI: https://doi.org/10.2210/pdb12US/pdb
• EM Map EMD-76770: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): adeno-associated virus 2, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2026-04-20 Released: 2026-09-30 
• Deposition Author(s): Zachery, J., Mietzsch, M., McKenna, R.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.28 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Broadly cross-reactive anti-capsid IgA is an overlooked antibody 1 barrier in AAV2 mediated gene transfer

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.

(2026) Nat Commun 

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Hetero 180-mer - A60B60C60 Pseudo Symmetry: Icosahedral - I  (Explore in 3D)
Pseudo Stoichiometry: Hetero 180-mer - A120B60 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 5,168.21 kDa 
• Atom Count: 358,740 
• Modeled Residue Count: 45,600 
• Deposited Residue Count: 46,500 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP1	A, AA [auth 1], AB [auth u], B, BA [auth 2], BB [auth v], C, CA [auth 3], CB [auth w], D, DA [auth 4], DB [auth x], E, EA [auth 5], EB [auth y], F, FA [auth 6], FB [auth z], G, GA [auth a], GB [auth 7], H, HA [auth b], HB [auth 8], I, IA [auth c], J, JA [auth d], K, KA [auth e], L, LA [auth f], M, MA [auth g], N, NA [auth h], O, OA [auth i], P, PA [auth j], Q, QA [auth k], R, RA [auth l], S, SA [auth m], T, TA [auth n], U, UA [auth o], V, VA [auth p], W, WA [auth q], X, XA [auth r], Y, YA [auth s], Z, ZA [auth t]	533	adeno-associated virus 2	Mutation(s): 0  Gene Names: VP1
UniProt
Find proteins for P03135 (Adeno-associated virus 2 (isolate Srivastava/1982)) Explore P03135  Go to UniProtKB:  P03135

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab3-2 IgG Heavy chain	AC [auth Sh], AD [auth mh], BC [auth Th], BD [auth nh], CC [auth Uh], CD [auth oh], DC [auth Vh], DD [auth ph], EC [auth Wh], ED [auth qh], FC [auth Xh], FD [auth rh], GC [auth Yh], GD [auth sh], HC [auth Zh], HD [auth th], IB [auth Ah], IC [auth 1h], ID [auth uh], JB [auth Bh], JC [auth 2h], JD [auth vh], KB [auth Ch], KC [auth 3h], KD [auth wh], LB [auth Dh], LC [auth 4h], LD [auth xh], MB [auth Eh], MC [auth 5h], MD [auth yh], NB [auth Fh], NC [auth 6h], ND [auth zh], OB [auth Gh], OC [auth ah], OD [auth 7h], PB [auth Hh], PC [auth bh], PD [auth 8h], QB [auth Ih], QC [auth ch], RB [auth Jh], RC [auth dh], SB [auth Kh], SC [auth eh], TB [auth Lh], TC [auth fh], UB [auth Mh], UC [auth gh], VB [auth Nh], VC [auth hh], WB [auth Oh], WC [auth ih], XB [auth Ph], XC [auth jh], YB [auth Qh], YC [auth kh], ZB [auth Rh], ZC [auth lh]	132	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab3-2 IgG Light Chain	AE [auth Kl], AF [auth el], BE [auth Ll], BF [auth fl], CE [auth Ml], CF [auth gl], DE [auth Nl], DF [auth hl], EE [auth Ol], EF [auth il], FE [auth Pl], FF [auth jl], GE [auth Ql], GF [auth kl], HE [auth Rl], HF [auth ll], IE [auth Sl], IF [auth ml], JE [auth Tl], JF [auth nl], KE [auth Ul], KF [auth ol], LE [auth Vl], LF [auth pl], ME [auth Wl], MF [auth ql], NE [auth Xl], NF [auth rl], OE [auth Yl], OF [auth sl], PE [auth Zl], PF [auth tl], QD [auth Al], QE [auth 1l], QF [auth ul], RD [auth Bl], RE [auth 2l], RF [auth vl], SD [auth Cl], SE [auth 3l], SF [auth wl], TD [auth Dl], TE [auth 4l], TF [auth xl], UD [auth El], UE [auth 5l], UF [auth yl], VD [auth Fl], VE [auth 6l], VF [auth zl], WD [auth Gl], WE [auth al], WF [auth 7l], XD [auth Hl], XE [auth bl], XF [auth 8l], YD [auth Il], YE [auth cl], ZD [auth Jl], ZE [auth dl]	110	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.28 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.10-2155_2155
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-30 
Deposition Author(s): Zachery, J., Mietzsch, M., McKenna, R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM082946

Revision History  

• Version 1.0: 2026-09-30
  Type: Initial release