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- EMDB-9796: AAV5 in complex with AAVR -

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Basic information

Entry
Database: EMDB / ID: EMD-9796
TitleAAV5 in complex with AAVR
Map data
Sample
  • Complex: Adeno-associated virus - 5
    • Complex: capsid protein VP1
      • Protein or peptide: Capsid protein
    • Organelle or cellular component: PKD1
      • Protein or peptide: Dyslexia-associated protein KIAA0319-like protein
Keywordsadeno-associated virus / AAV5 / receptor / AAVR / VIRUS
Function / homology
Function and homology information


proacrosomal vesicle fusion / response to auditory stimulus / flagellated sperm motility / T=1 icosahedral viral capsid / receptor-mediated endocytosis of virus by host cell / trans-Golgi network / neuron migration / cytoplasmic vesicle / Golgi membrane / nucleolus ...proacrosomal vesicle fusion / response to auditory stimulus / flagellated sperm motility / T=1 icosahedral viral capsid / receptor-mediated endocytosis of virus by host cell / trans-Golgi network / neuron migration / cytoplasmic vesicle / Golgi membrane / nucleolus / structural molecule activity / Golgi apparatus / membrane / plasma membrane
Similarity search - Function
Dyslexia-associated protein KIAA0319-like / : / Dyslexia-associated protein KIAA0319 N-terminal domain / KIAA0319 C-terminal domain / MANSC domain / MANSC domain profile. / K319L-like, PKD domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily ...Dyslexia-associated protein KIAA0319-like / : / Dyslexia-associated protein KIAA0319 N-terminal domain / KIAA0319 C-terminal domain / MANSC domain / MANSC domain profile. / K319L-like, 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 VP1/VP2 / Capsid/spike protein, ssDNA virus / Immunoglobulin-like fold
Similarity search - Domain/homology
Dyslexia-associated protein KIAA0319-like protein / Capsid protein
Similarity search - Component
Biological speciesAdeno-associated virus - 5 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsLou Z / Zhang R
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China China
CitationJournal: Nat Commun / Year: 2019
Title: Divergent engagements between adeno-associated viruses with their cellular receptor AAVR.
Authors: Ran Zhang / Guangxue Xu / Lin Cao / Zixian Sun / Yong He / Mengtian Cui / Yuna Sun / Shentao Li / Huapeng Li / Lan Qin / Mingxu Hu / Zhengjia Yuan / Zipei Rao / Wei Ding / Zihe Rao / Zhiyong Lou /
Abstract: Adeno-associated virus (AAV) receptor (AAVR) is an essential receptor for the entry of multiple AAV serotypes with divergent rules; however, the mechanism remains unclear. Here, we determine the ...Adeno-associated virus (AAV) receptor (AAVR) is an essential receptor for the entry of multiple AAV serotypes with divergent rules; however, the mechanism remains unclear. Here, we determine the structures of the AAV1-AAVR and AAV5-AAVR complexes, revealing the molecular details by which PKD1 recognizes AAV5 and PKD2 is solely engaged with AAV1. PKD2 lies on the plateau region of the AAV1 capsid. However, the AAV5-AAVR interface is strikingly different, in which PKD1 is bound at the opposite side of the spike of the AAV5 capsid than the PKD2-interacting region of AAV1. Residues in strands F/G and the CD loop of PKD1 interact directly with AAV5, whereas residues in strands B/C/E and the BC loop of PKD2 make contact with AAV1. These findings further the understanding of the distinct mechanisms by which AAVR recognizes various AAV serotypes and provide an example of a single receptor engaging multiple viral serotypes with divergent rules.
History
DepositionJan 30, 2019-
Header (metadata) releaseAug 7, 2019-
Map releaseAug 14, 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: 0.03
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  • Surface view colored by radius
  • Surface level: 0.03
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  • Surface view with fitted model
  • Atomic models: PDB-6jcs
  • Surface level: 0.03
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6jcs
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9796.png

Downloads & links

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Map

FileDownload / File: emd_9796.map.gz / Format: CCP4 / Size: 209.3 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 380 pix.
= 353.4 Å		0.93 Å/pix.
x 380 pix.
= 353.4 Å		0.93 Å/pix.
x 380 pix.
= 353.4 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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.12124219 - 0.24112643
Average (Standard dev.)0.004192867 (±0.017954214)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-189-189-189
Dimensions380380380
Spacing380380380
CellA=B=C: 353.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.930.930.93
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z353.400353.400353.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS-189-189-189
NC/NR/NS380380380
D min/max/mean-0.1210.2410.004

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Supplemental data

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Sample components

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Entire : Adeno-associated virus - 5

EntireName: Adeno-associated virus - 5
Components
  • Complex: Adeno-associated virus - 5
    • Complex: capsid protein VP1
      • Protein or peptide: Capsid protein
    • Organelle or cellular component: PKD1
      • Protein or peptide: Dyslexia-associated protein KIAA0319-like protein

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Supramolecule #1: Adeno-associated virus - 5

SupramoleculeName: Adeno-associated virus - 5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: capsid protein VP1

SupramoleculeName: capsid protein VP1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Adeno-associated virus - 5

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Supramolecule #3: PKD1

SupramoleculeName: PKD1 / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Adeno-associated virus - 5
Molecular weightTheoretical: 58.213078 KDa
SequenceString: DGVGNASGDW HCDSTWMGDR VVTKSTRTWV LPSYNNHQYR EIKSGSVDGS NANAYFGYST PWGYFDFNRF HSHWSPRDWQ RLINNYWGF RPRSLRVKIF NIQVKEVTVQ DSTTTIANNL TSTVQVFTDD DYQLPYVVGN GTEGCLPAFP PQVFTLPQYG Y ATLNRDNT ...String:
DGVGNASGDW HCDSTWMGDR VVTKSTRTWV LPSYNNHQYR EIKSGSVDGS NANAYFGYST PWGYFDFNRF HSHWSPRDWQ RLINNYWGF RPRSLRVKIF NIQVKEVTVQ DSTTTIANNL TSTVQVFTDD DYQLPYVVGN GTEGCLPAFP PQVFTLPQYG Y ATLNRDNT ENPTERSSFF CLEYFPSKML RTGNNFEFTY NFEEVPFHSS FAPSQNLFKL ANPLVDQYLY RFVSTNNTGG VQ FNKNLAG RYANTYKNWF PGPMGRTQGW NLGSGVNRAS VSAFATTNRM ELEGASYQVP PQPNGMTNNL QGSNTYALEN TMI FNSQPA NPGTTATYLE GNMLITSESE TQPVNRVAYN VGGQMATNNQ SSTTAPATGT YNLQEIVPGS VWMERDVYLQ GPIW AKIPE TGAHFHPSPA MGGFGLKHPP PMMLIKNTPV PGNITSFSDV PVSSFITQYS TGQVTVEMEW ELKKENSKRW NPEIQ YTNN YNDPQFVDFA PDSTGEYRTT RPIGTRYLTR PL

UniProtKB: Capsid protein

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Macromolecule #2: Dyslexia-associated protein KIAA0319-like protein

MacromoleculeName: Dyslexia-associated protein KIAA0319-like protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.911322 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
VIKELVVSAG ESVQITLPKN EVQLNAYVLQ EPPKGETYTY DWQLITHPRD YSGEMEGKHS QILKLSKLTP GLYEFKVIVE GQNAHGEGY VNVTVKPE

UniProtKB: Dyslexia-associated protein KIAA0319-like protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state2D array

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 36.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12590
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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