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- EMDB-9672: Adeno-Associated Virus 2 in complex with AAVR -

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Basic information

Entry
Database: EMDB / Id: 9672
TitleAdeno-Associated Virus 2 in complex with AAVR
Map data
SampleAAV2 in complex with AAVR
  • Adeno-associated virus 2
  • AAVR PKD2
  • Dyslexia-associated protein KIAA0319-like protein
  • Capsid protein VP1
Func 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
SourceAdeno-associated virus 2 (isolate Srivastava/1982) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsLou ZY / Zhang R
CitationJournal: Nat Microbiol / Year: 2019
Title: Adeno-associated virus 2 bound to its cellular receptor AAVR.
P-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 ReportPDB-ID: 6ihb

SummaryFull reportAbout validation report
DateDeposition: Sep 29, 2018 / Header (metadata) release: Mar 20, 2019 / Map release: Mar 20, 2019 / Last update: Apr 10, 2019

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Strvis

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0025
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6ihb
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6ihb
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downlink

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Map

Fileemd_9672.map.gz (map file in CCP4 format, 340737 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
440 pix
0.93 Å/pix.
= 409.2 Å
440 pix
0.93 Å/pix.
= 409.2 Å
440 pix
0.93 Å/pix.
= 409.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density
Contour Level:0.0025 (by author), 0.0025 (movie #1):
Minimum - Maximum-0.14267884 - 0.14006905
Average (Standard dev.)0.0010085038 (0.00828199)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions440440440
Origin-220.0-220.0-220.0
Limit219.0219.0219.0
Spacing440440440
CellA=B=C: 409.2 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.930.930.93
M x/y/z440440440
origin x/y/z0.0000.0000.000
length x/y/z409.200409.200409.200
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-220-220-220
NC/NR/NS440440440
D min/max/mean-0.1430.1400.001

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Supplemental data

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Sample components

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Entire AAV2 in complex with AAVR

EntireName: AAV2 in complex with AAVR / Number of components: 5

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Component #1: protein, AAV2 in complex with AAVR

ProteinName: AAV2 in complex with AAVR / Recombinant expression: No

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Component #2: protein, Adeno-associated virus 2

ProteinName: Adeno-associated virus 2 / Recombinant expression: No
SourceSpecies: Adeno-associated virus 2 (isolate Srivastava/1982)

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Component #3: protein, AAVR PKD2

ProteinName: AAVR PKD2 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #4: protein, Dyslexia-associated protein KIAA0319-like protein

ProteinName: Dyslexia-associated protein KIAA0319-like protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.31445 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #5: protein, Capsid protein VP1

ProteinName: Capsid protein VP1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 82.031352 kDa
SourceSpecies: Adeno-associated virus 2 (isolate Srivastava/1982)

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Experimental details

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Sample preparation

SpecimenSpecimen state: 2D array / Method: cryo EM
Sample solutionPh: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 1.53 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 16820
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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