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- PDB-7wjw: Structure of Adeno-associated virus serotype 9 -

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Basic information

Entry
Database: PDB / ID: 7wjw
TitleStructure of Adeno-associated virus serotype 9
ComponentsCapsid protein VP1
KeywordsVIRUS / Adeno-associated virus
Function / homologyPhospholipase 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 / T=1 icosahedral viral capsid / structural molecule activity / Capsid protein VP1
Function and homology information
Biological speciesAdeno-associated virus 9
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.87 Å
AuthorsXu, G. / Lou, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mol Ther Methods Clin Dev / Year: 2022
Title: Structural basis for the neurotropic AAV9 and the engineered AAVPHP.eB recognition with cellular receptors.
Authors: Guangxue Xu / Ran Zhang / Huapeng Li / Kaixin Yin / Xinyi Ma / Zhiyong Lou /
Abstract: Clade F adeno-associated virus (AAV) 9 has been utilized as therapeutic gene delivery vector, and it is capable of crossing blood brain barrier (BBB). Recently, an AAV9-based engineering serotype ...Clade F adeno-associated virus (AAV) 9 has been utilized as therapeutic gene delivery vector, and it is capable of crossing blood brain barrier (BBB). Recently, an AAV9-based engineering serotype AAVPHP.eB with enhanced BBB crossing ability further expanded clade F AAVs' usages in the murine central nervous system (CNS) gene delivery. In this study, we determined the cryo-electron microscopy (cryo-EM) structures of the AAVPHP.eB and its parental serotype AAV9 in native form or in complex with their essential receptor AAV receptor (AAVR). These structures reveal the molecular details of their AAVR recognition, where the polycystic kidney disease repeat domain 2 (PKD2) of AAVR interacts with AAV9 and AAVPHP.eB virions at the 3-fold protrusions and the raised capsid regions between the 2- and 5-fold axes, termed the 2/5-fold wall. The interacting patterns of AAVR to AAV9 and AAVPHP.eB are similar to what was observed in AAV1/AAV2-AAVR complexes. Moreover, we found that the AAVPHP.eB variable region VIII (VR-VIII) may independently facilitate the new receptor recognition responsible for enhanced CNS transduction. Our study provides insights into the recognition principles of multiple receptors for engineered AAVPHP.eB and parental serotype AAV9, and further reveal the potential molecular basis underlying their different tropisms.
History
DepositionJan 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 26, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / em_admin
Item: _citation.country / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein VP1


Theoretical massNumber of molelcules
Total (without water)58,4741
Polymers58,4741
Non-polymers00
Water00
1
A: Capsid protein VP1
x 60


  • complete icosahedral assembly
  • Evidence: electron microscopy
  • 3.51 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)3,508,46560
Polymers3,508,46560
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Capsid protein VP1
x 5


  • icosahedral pentamer
  • 292 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)292,3725
Polymers292,3725
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein VP1
x 6


  • icosahedral 23 hexamer
  • 351 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)350,8466
Polymers350,8466
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Capsid protein VP1


Mass: 58474.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Adeno-associated virus 9 / Gene: cap / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q6JC40

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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 9 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Adeno-associated virus 9
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293
Details of virusEmpty: YES / Enveloped: NO / Isolate: SEROTYPE / Type: VIRION
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

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 35.7 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24820 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0054257
ELECTRON MICROSCOPYf_angle_d0.5775802
ELECTRON MICROSCOPYf_dihedral_angle_d12.251565
ELECTRON MICROSCOPYf_chiral_restr0.042593
ELECTRON MICROSCOPYf_plane_restr0.004775

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