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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 / homologyParvovirus coat protein VP1, N-terminal / PKD domain / PKD domain superfamily / Dyslexia-associated protein KIAA0319-like protein / PKD/Chitinase domain / Capsid/spike protein, ssDNA virus / MANSC domain / Immunoglobulin-like fold / Parvovirus coat protein VP1 / Parvovirus coat protein VP2 ...Parvovirus coat protein VP1, N-terminal / PKD domain / PKD domain superfamily / Dyslexia-associated protein KIAA0319-like protein / PKD/Chitinase domain / Capsid/spike protein, ssDNA virus / MANSC domain / Immunoglobulin-like fold / Parvovirus coat protein VP1 / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Polycystic kidney disease (PKD) domain profile. / MANSC domain profile. / T=1 icosahedral viral capsid / permeabilization of host organelle membrane involved in viral entry into host cell / viral entry via permeabilization of inner membrane / host cell nucleolus / cytoplasmic vesicle / clathrin-dependent endocytosis of virus by host cell / virion attachment to host cell / Golgi membrane / structural molecule activity / integral component of membrane / plasma membrane / Capsid protein VP1 / Dyslexia-associated protein KIAA0319-like protein
Function and homology information
Specimen sourceHomo sapiens (human)
Adeno-associated virus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsLou, Z.Y. / Zhang, R.
Funding supportChina , 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China21572116China
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 29, 2018 / Release: Mar 20, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 20, 2019Structure modelrepositoryInitial release
1.1Apr 10, 2019Structure modelData collection / Database referencescitation / citation_author_citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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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Structure viewerMolecule:
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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
Polyers92,3462
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
Polyers5,540,748120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
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
Polyers461,72910
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
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
Polyers554,07512
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1

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Components

#1: Protein/peptide Dyslexia-associated protein KIAA0319-like protein / Adeno-associated virus receptor / AAVR


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


Mass: 82031.352 Da / Num. of mol.: 1
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

Type: COMPLEX

IDNameEntity IDParent-IDSource
1AAV2 in complex with AAVR1, 20MULTIPLE SOURCES
2Adeno-associated virus 221NATURAL
3AAVR PKD211RECOMBINANT
Source (natural)
IDEntity assembly-IDNcbi tax-IDOrganism
12648242Adeno-associated virus 2 (isolate Srivastava/1982)
239606Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Details of virusEmpty: YES / Enveloped: NO / Virus isolate: STRAIN / Virus 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

Refinement-ID: ELECTRON MICROSCOPY

TypeDev idealNumber
f_bond_d0.0089271
f_angle_d0.95612643
f_dihedral_angle_d6.8775455
f_chiral_restr0.0571337
f_plane_restr0.0081673

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