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- PDB-9zcw: Cryo-EM structure of the engineered vector AAV2.ATX002 -

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Basic information

Entry
Database: PDB / ID: 9zcw
TitleCryo-EM structure of the engineered vector AAV2.ATX002
ComponentsEngineered AAV2 capsid protein VP3
KeywordsVIRUS / Adeno-Associated Virus / AAV / Engineered AAV / AAV2
Function / homology
Function and homology information


symbiont entry into host cell via permeabilization of host membrane / host cell nucleolus / T=1 icosahedral viral capsid / 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
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.9 Å
AuthorsBetegon, M. / Byrne, L.C. / Conway, J.F.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)UH3MH120094 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)UF1MH130881 United States
National Institutes of Health/National Eye Institute (NIH/NEI)P30 EY08098 United States
National Institutes of Health/Office of the DirectorS10OD019995 United States
National Institutes of Health/Office of the DirectorS10OD025009 United States
CitationJournal: To Be Published
Title: Structural dynamics insights into principles underlying the increased fitness of newly engineered and broadly potent AAV capsids
Authors: Johnson, M.E. / Ozturk, B.E. / Tugwell, T.H. / Lambros, M. / Janowitz, H. / Sedorovitz, M. / Flohr, K. / Campello, L. / Hartung, J.E. / Hogle, B. / Gillespie, M. / Schriever, H. / Aweidah, H. ...Authors: Johnson, M.E. / Ozturk, B.E. / Tugwell, T.H. / Lambros, M. / Janowitz, H. / Sedorovitz, M. / Flohr, K. / Campello, L. / Hartung, J.E. / Hogle, B. / Gillespie, M. / Schriever, H. / Aweidah, H. / Koester, J. / Clausen, I. / Seeber, S. / Revelant, F. / Schreurs, R. / Koechl, F. / Sieving, P.A. / Sahel, J.A. / Stauffer, W.R. / Peixoto, R.T. / Fauser, S. / Lin, R. / Conway, J. / Da Silva, S. / Krol, J. / Betegon, M. / Byrne, L.C.
History
DepositionNov 24, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Engineered AAV2 capsid protein VP3
2: Engineered AAV2 capsid protein VP3
3: Engineered AAV2 capsid protein VP3
4: Engineered AAV2 capsid protein VP3
5: Engineered AAV2 capsid protein VP3
6: Engineered AAV2 capsid protein VP3
7: Engineered AAV2 capsid protein VP3
8: Engineered AAV2 capsid protein VP3
A: Engineered AAV2 capsid protein VP3
B: Engineered AAV2 capsid protein VP3
C: Engineered AAV2 capsid protein VP3
D: Engineered AAV2 capsid protein VP3
E: Engineered AAV2 capsid protein VP3
F: Engineered AAV2 capsid protein VP3
G: Engineered AAV2 capsid protein VP3
H: Engineered AAV2 capsid protein VP3
I: Engineered AAV2 capsid protein VP3
J: Engineered AAV2 capsid protein VP3
K: Engineered AAV2 capsid protein VP3
L: Engineered AAV2 capsid protein VP3
M: Engineered AAV2 capsid protein VP3
N: Engineered AAV2 capsid protein VP3
O: Engineered AAV2 capsid protein VP3
P: Engineered AAV2 capsid protein VP3
Q: Engineered AAV2 capsid protein VP3
R: Engineered AAV2 capsid protein VP3
S: Engineered AAV2 capsid protein VP3
T: Engineered AAV2 capsid protein VP3
U: Engineered AAV2 capsid protein VP3
V: Engineered AAV2 capsid protein VP3
W: Engineered AAV2 capsid protein VP3
X: Engineered AAV2 capsid protein VP3
Y: Engineered AAV2 capsid protein VP3
Z: Engineered AAV2 capsid protein VP3
a: Engineered AAV2 capsid protein VP3
b: Engineered AAV2 capsid protein VP3
c: Engineered AAV2 capsid protein VP3
d: Engineered AAV2 capsid protein VP3
e: Engineered AAV2 capsid protein VP3
f: Engineered AAV2 capsid protein VP3
g: Engineered AAV2 capsid protein VP3
h: Engineered AAV2 capsid protein VP3
i: Engineered AAV2 capsid protein VP3
j: Engineered AAV2 capsid protein VP3
k: Engineered AAV2 capsid protein VP3
l: Engineered AAV2 capsid protein VP3
m: Engineered AAV2 capsid protein VP3
n: Engineered AAV2 capsid protein VP3
o: Engineered AAV2 capsid protein VP3
p: Engineered AAV2 capsid protein VP3
q: Engineered AAV2 capsid protein VP3
r: Engineered AAV2 capsid protein VP3
s: Engineered AAV2 capsid protein VP3
t: Engineered AAV2 capsid protein VP3
u: Engineered AAV2 capsid protein VP3
v: Engineered AAV2 capsid protein VP3
w: Engineered AAV2 capsid protein VP3
x: Engineered AAV2 capsid protein VP3
y: Engineered AAV2 capsid protein VP3
z: Engineered AAV2 capsid protein VP3


Theoretical massNumber of molelcules
Total (without water)3,668,41260
Polymers3,668,41260
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 ...
Engineered AAV2 capsid protein VP3


Mass: 61140.199 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Details: Engineered AAV2 capsid VP3 protein with a 9AA insertion.
Source: (gene. exp.) adeno-associated virus 2 / Gene: VP1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P03135
Has protein modificationN

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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: adeno-associated virus 2 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: adeno-associated virus 2
Source (recombinant)Organism: Homo sapiens (human) / Strain: 293AAV
Details of virusEmpty: NO / Enveloped: NO / Isolate: SEROTYPE / Type: VIRION
Buffer solutionpH: 7.4 / Details: DPBS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 95 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.43 sec. / Electron dose: 30 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10377
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategoryFitting-ID
1Topaz0.3particle selection
2EPU3.7.1image acquisition
4CTFFIND4.1.14CTF correction
10UCSF ChimeraX1.10.1model fitting1
11PHENIX1.21model refinement1
14RELION5initial Euler assignment
15RELION5final Euler assignment
16RELION5classification
17RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 160533
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 1.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14969 / Algorithm: BACK PROJECTION / Details: Ewald sphere correction applied in RELION 5.0 / Symmetry type: POINT
Atomic model building
IDProtocolSpaceTarget criteriaDetails
1FLEXIBLE FITREALCross-correlation
2AB INITIO MODELAb initio model created with ModelAngelo
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameTypeDetails
16U0R

6u0r

16U0R1PDBexperimental model
22OtherotherModelAngelo
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 37.63 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0051260400
ELECTRON MICROSCOPYf_angle_d0.595355080
ELECTRON MICROSCOPYf_chiral_restr0.043637020
ELECTRON MICROSCOPYf_plane_restr0.004247160
ELECTRON MICROSCOPYf_dihedral_angle_d5.898834729

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