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- PDB-6ihb: Adeno-Associated Virus 2 in complex with AAVR -

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Basic information

Entry
Database: PDB / ID: 6ihb
TitleAdeno-Associated Virus 2 in complex with AAVR
Components
  • Capsid protein VP1
  • Dyslexia-associated protein KIAA0319-like protein
KeywordsVIRUS / AAV2
Function / homology
Function and homology information


permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / host cell nucleolus / T=1 icosahedral viral capsid / neuron migration / cytoplasmic vesicle / clathrin-dependent endocytosis of virus by host cell / Golgi membrane / virion attachment to host cell / nucleolus ...permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / host cell nucleolus / T=1 icosahedral viral capsid / neuron migration / cytoplasmic vesicle / clathrin-dependent endocytosis of virus by host cell / Golgi membrane / virion attachment to host cell / nucleolus / structural molecule activity / Golgi apparatus / membrane / plasma membrane
Similarity search - Function
Dyslexia-associated protein KIAA0319-like / MANSC domain / MANSC domain profile. / Empty Capsid Viral Protein 2 / Parvovirus coat protein VP1/VP2 / PKD domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain ...Dyslexia-associated protein KIAA0319-like / MANSC domain / MANSC domain profile. / Empty Capsid Viral Protein 2 / Parvovirus coat protein VP1/VP2 / PKD domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / 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 / Beta Complex / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
Capsid protein VP1 / Dyslexia-associated protein KIAA0319-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Adeno-associated virus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsLou, Z.Y. / Zhang, R.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China21572116 China
CitationJournal: Nat Microbiol / Year: 2019
Title: Adeno-associated virus 2 bound to its cellular receptor AAVR.
Authors: Ran Zhang / Lin Cao / Mengtian Cui / Zixian Sun / Mingxu Hu / Rouxuan Zhang / William Stuart / Xiaochu Zhao / Zirui Yang / Xueming Li / Yuna Sun / Shentao Li / Wei Ding / Zhiyong Lou / Zihe Rao /
Abstract: Adeno-associated virus (AAV) is a leading vector for virus-based gene therapy. The receptor for AAV (AAVR; also named KIAA0319L) was recently identified, and the precise characterization of AAV-AAVR ...Adeno-associated virus (AAV) is a leading vector for virus-based gene therapy. The receptor for AAV (AAVR; also named KIAA0319L) was recently identified, and the precise characterization of AAV-AAVR recognition is in immediate demand. Taking advantage of a particle-filtering algorithm, we report here the cryo-electron microscopy structure of the AAV2-AAVR complex at 2.8 Å resolution. This structure reveals that of the five Ig-like polycystic kidney disease (PKD) domains in AAVR, PKD2 binds directly to the spike region of the AAV2 capsid adjacent to the icosahedral three-fold axis. Residues in strands B and E, and the BC loop of AAVR PKD2 interact directly with the AAV2 capsid. The interacting residues in the AAV2 capsid are mainly in AAV-featured variable regions. Mutagenesis of the amino acids at the AAV2-AAVR interface reduces binding activity and viral infectivity. Our findings provide insights into the biology of AAV entry with high-resolution details, providing opportunities for the development of new AAV vectors for gene therapy.
History
DepositionSep 29, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Assembly

Deposited unit
R: Dyslexia-associated protein KIAA0319-like protein
A: Capsid protein VP1


Theoretical massNumber of molelcules
Total (without water)92,3462
Polymers92,3462
Non-polymers00
Water0
1
R: Dyslexia-associated protein KIAA0319-like protein
A: Capsid protein VP1
x 60


Theoretical massNumber of molelcules
Total (without water)5,540,748120
Polymers5,540,748120
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
R: Dyslexia-associated protein KIAA0319-like protein
A: Capsid protein VP1
x 5


  • icosahedral pentamer
  • 462 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)461,72910
Polymers461,72910
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
R: Dyslexia-associated protein KIAA0319-like protein
A: Capsid protein VP1
x 6


  • icosahedral 23 hexamer
  • 554 kDa, 12 polymers
Theoretical massNumber of molelcules
Total (without water)554,07512
Polymers554,07512
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 Dyslexia-associated protein KIAA0319-like protein / Adeno-associated virus receptor / AAVR


Mass: 10314.450 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0319L, AAVR, KIAA1837, PP791 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IZA0
#2: Protein Capsid protein VP1 /


Mass: 82031.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Adeno-associated virus 2 (isolate Srivastava/1982)
References: UniProt: P03135

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1AAV2 in complex with AAVRAdeno-associated virusCOMPLEXall0MULTIPLE SOURCES
2Adeno-associated virus 2COMPLEX#21NATURAL
3AAVR PKD2COMPLEX#11RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Adeno-associated virus 2 (isolate Srivastava/1982)648242
23Homo sapiens (human)9606
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.5
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 FIELDBright-field microscopy
Image recordingElectron dose: 1.53 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16820 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0089271
ELECTRON MICROSCOPYf_angle_d0.95612643
ELECTRON MICROSCOPYf_dihedral_angle_d6.8775455
ELECTRON MICROSCOPYf_chiral_restr0.0571337
ELECTRON MICROSCOPYf_plane_restr0.0081673

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