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- PDB-9j7k: Structure of AAV8 in the complex of AAV8 with its receptor -

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Basic information

Entry
Database: PDB / ID: 9j7k
TitleStructure of AAV8 in the complex of AAV8 with its receptor
ComponentsCapsid protein
KeywordsVIRUS / AAV8 / complex
Function / homology
Function and homology information


T=1 icosahedral viral capsid / nucleotide binding / 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 VP2 / Capsid/spike protein, ssDNA virus
Similarity search - Domain/homology
Biological speciesAdeno-associated virus - 8
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.32 Å
AuthorsXu, H. / Wang, G.P. / Su, X.D.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFC2301402 China
CitationJournal: Cell / Year: 2025
Title: An alternate receptor for adeno-associated viruses.
Authors: Bijay P Dhungel / Hua Xu / Rajini Nagarajah / Joseph Vitale / Alex C H Wong / Divya Gokal / Yue Feng / Mehdi Sharifi Tabar / Cynthia Metierre / Chirag Parsania / Xiaohui Song / Guopeng Wang ...Authors: Bijay P Dhungel / Hua Xu / Rajini Nagarajah / Joseph Vitale / Alex C H Wong / Divya Gokal / Yue Feng / Mehdi Sharifi Tabar / Cynthia Metierre / Chirag Parsania / Xiaohui Song / Guopeng Wang / Xiao-Dong Su / Charles G Bailey / John E J Rasko /
Abstract: Systemic gene therapy using adeno-associated virus (AAV) vectors is approved for the treatment of several genetic disorders, but challenges and toxicities associated with high vector doses remain. We ...Systemic gene therapy using adeno-associated virus (AAV) vectors is approved for the treatment of several genetic disorders, but challenges and toxicities associated with high vector doses remain. We report an alternate receptor for AAV (AAVR2, carboxypeptidase D [CPD]), which is distinct from the multi-serotype AAV receptor (AAVR). AAVR2 enables the transduction of clade E AAVs, including AAV8, and determines an exclusive AAVR-independent transduction pathway for AAV11 and AAV12. We characterized direct binding between the AAV8 capsid and AAVR2 by cryo-electron microscopy (cryo-EM) and identified contact residues. We observed that AAV8 directly binds to the carboxypeptidase-like domain 1 of AAVR2 via its variable region VIII and demonstrated that AAV capsids that lack AAVR2 binding can be bioengineered to engage with AAVR2. Finally, we overexpressed a minimal functional AAVR2 to enhance AAV transduction in vivo. Our study provides insights into AAV biology and clinically deployable solutions to reduce dose-related toxicities associated with AAV vectors.
History
DepositionAug 19, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed ..._citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,909,98360
Polymers4,909,98360
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Capsid protein


Mass: 81833.047 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adeno-associated virus - 8 / Production host: Homo sapiens (human) / References: UniProt: Q8JQF8
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 8 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: adeno-associated virus 8
Source (recombinant)Organism: Homo sapiens (human)
Details of virusEmpty: YES / Enveloped: NO / Isolate: SEROTYPE / Type: VIRION
Buffer solutionpH: 7.2
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 235305 / Symmetry type: POINT

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