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- PDB-9j6z: Structure of AAV8 in complex with its receptor -

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Basic information

Entry
Database: PDB / ID: 9j6z
TitleStructure of AAV8 in complex with its receptor
Components
  • Capsid protein
  • Carboxypeptidase D
KeywordsVIRAL PROTEIN/HYDROLASE / AAV8 / receptor / complex / VIRAL PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


metallocarboxypeptidase D / serine-type carboxypeptidase activity / peptide metabolic process / RND1 GTPase cycle / RND3 GTPase cycle / T=1 icosahedral viral capsid / Golgi Associated Vesicle Biogenesis / metallocarboxypeptidase activity / protein processing / nucleotide binding ...metallocarboxypeptidase D / serine-type carboxypeptidase activity / peptide metabolic process / RND1 GTPase cycle / RND3 GTPase cycle / T=1 icosahedral viral capsid / Golgi Associated Vesicle Biogenesis / metallocarboxypeptidase activity / protein processing / nucleotide binding / structural molecule activity / extracellular space / extracellular exosome / zinc ion binding / membrane / plasma membrane
Similarity search - Function
Carboxypeptidase D, carboxypeptidase-like domain 3 / Carboxypeptidase D, carboxypeptidase-like domain 2 / : / Carboxypeptidase regulatory-like domain / Carboxypeptidase-like, regulatory domain superfamily / Zinc carboxypeptidases, zinc-binding region 2 signature. / Zinc carboxypeptidases, zinc-binding region 1 signature. / Zn_pept / Zinc carboxypeptidase / Peptidase family M14 domain profile. ...Carboxypeptidase D, carboxypeptidase-like domain 3 / Carboxypeptidase D, carboxypeptidase-like domain 2 / : / Carboxypeptidase regulatory-like domain / Carboxypeptidase-like, regulatory domain superfamily / Zinc carboxypeptidases, zinc-binding region 2 signature. / Zinc carboxypeptidases, zinc-binding region 1 signature. / Zn_pept / Zinc carboxypeptidase / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A / 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
Carboxypeptidase D / Capsid protein
Similarity search - Component
Biological speciesAdeno-associated virus - 8
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.02 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 17, 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
5: Capsid protein
6: Capsid protein
7: Capsid protein
A: Carboxypeptidase D
c: Capsid protein
o: Capsid protein
p: Capsid protein


Theoretical massNumber of molelcules
Total (without water)541,9847
Polymers541,9847
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.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adeno-associated virus - 8 / Production host: Homo sapiens (human) / References: UniProt: Q8JQF8
#2: Protein Carboxypeptidase D / Metallocarboxypeptidase D / gp180


Mass: 50985.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CPD / Production host: Homo sapiens (human) / References: UniProt: O75976, metallocarboxypeptidase D
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: AAV8 in complex with receptor / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Adeno-associated virus - 8202813
31Homo sapiens (human)9606
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.2
SpecimenEmbedding 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: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30953 / Symmetry type: POINT

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