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- EMDB-9671: Adeno-Associated Virus 2 at 2.8 ang -

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Basic information

Entry
Database: EMDB / ID: EMD-9671
TitleAdeno-Associated Virus 2 at 2.8 ang
Map data
Sample
  • Virus: Ao-associated virus 2 (isolate Srivastava/1982)
    • Protein or peptide: Capsid protein VP1
KeywordsAAV2 / VIRUS
Function / homology
Function and homology information


symbiont entry into host cell via permeabilization of host membrane / host cell nucleolus / T=1 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / virion attachment to host cell / structural molecule activity
Similarity search - Function
Phospholipase A2-like domain / Phospholipase A2-like domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP1/VP2 / Capsid/spike protein, ssDNA virus
Similarity search - Domain/homology
Biological speciesAdeno-associated virus 2 (isolate Srivastava/1982) / Ao-associated virus 2 (isolate Srivastava/1982)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsLou ZY / Zhang R
Funding support China, 1 items
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, 2018-
Header (metadata) releaseJun 26, 2019-
Map releaseJul 3, 2019-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.01
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  • Surface view with fitted model
  • Atomic models: PDB-6ih9
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ih9
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9671.png

Downloads & links

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Map

FileDownload / File: emd_9671.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 440 pix.
= 410.08 Å		0.93 Å/pix.
x 440 pix.
= 410.08 Å		0.93 Å/pix.
x 440 pix.
= 410.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.26006162 - 0.4412
Average (Standard dev.)0.001723597 (±0.022882227)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-219-219-219
Dimensions440440440
Spacing440440440
CellA=B=C: 410.08 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.9320.9320.932
M x/y/z440440440
origin x/y/z0.0000.0000.000
length x/y/z410.080410.080410.080
α/β/γ90.00090.00090.000
start NX/NY/NZ-100-100-99
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS-219-219-219
NC/NR/NS440440440
D min/max/mean-0.2600.4410.002

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Supplemental data

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Sample components

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Entire : Ao-associated virus 2 (isolate Srivastava/1982)

EntireName: Ao-associated virus 2 (isolate Srivastava/1982)
Components
  • Virus: Ao-associated virus 2 (isolate Srivastava/1982)
    • Protein or peptide: Capsid protein VP1

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Supramolecule #1: Ao-associated virus 2 (isolate Srivastava/1982)

SupramoleculeName: Ao-associated virus 2 (isolate Srivastava/1982) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 648242
Sci species name: Ao-associated virus 2 (isolate Srivastava/1982)
Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Virus shellShell ID: 1 / Diameter: 280.0 Å

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Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Adeno-associated virus 2 (isolate Srivastava/1982)
Strain: isolate Srivastava/1982
Molecular weightTheoretical: 58.644492 KDa
SequenceString: DGVGNSSGNW HCDSTWMGDR VITTSTRTWA LPTYNNHLYK QISSQSGASN DNHYFGYSTP WGYFDFNRFH CHFSPRDWQR LINNNWGFR PKRLNFKLFN IQVKEVTQND GTTTIANNLT STVQVFTDSE YQLPYVLGSA HQGCLPPFPA DVFMVPQYGY L TLNNGSQA ...String:
DGVGNSSGNW HCDSTWMGDR VITTSTRTWA LPTYNNHLYK QISSQSGASN DNHYFGYSTP WGYFDFNRFH CHFSPRDWQR LINNNWGFR PKRLNFKLFN IQVKEVTQND GTTTIANNLT STVQVFTDSE YQLPYVLGSA HQGCLPPFPA DVFMVPQYGY L TLNNGSQA VGRSSFYCLE YFPSQMLRTG NNFTFSYTFE DVPFHSSYAH SQSLDRLMNP LIDQYLYYLS RTNTPSGTTT QS RLQFSQA GASDIRDQSR NWLPGPCYRQ QRVSKTSADN NNSEYSWTGA TKYHLNGRDS LVNPGPAMAS HKDDEEKFFP QSG VLIFGK QGSEKTNVDI EKVMITDEEE IRTTNPVATE QYGSVSTNLQ RGNRQAATAD VNTQGVLPGM VWQDRDVYLQ GPIW AKIPH TDGHFHPSPL MGGFGLKHPP PQILIKNTPV PANPSTTFSA AKFASFITQY STGQVSVEIE WELQKENSKR WNPEI QYTS NYNKSVNVDF TVDTNGVYSE PRPIGTRYLT RNL

UniProtKB: Capsid protein VP1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK I
DetailsThe AAV2 particles are purified fron 293T cell, with the yeild of approximately 10^12vg per 10L.

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Digitization - Frames/image: 1-19 / Number grids imaged: 1 / Average exposure time: 1.2 sec. / Average electron dose: 1.53 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Software - details: CTFFIND4.1 was used to determine the CTF correction.
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1)
Software - details: RELION2.1 was used for the final reconstruction software.
Number images used: 14434
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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