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- EMDB-32712: Adeno-associated virus serotype PHP.eB in complex with AAVR -

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Basic information

Entry
Database: EMDB / ID: EMD-32712
TitleAdeno-associated virus serotype PHP.eB in complex with AAVR
Map data
Sample
  • Complex: Adeno-associated virus 9
    • Complex: Dyslexia-associated protein KIAA0319-like protein
      • Protein or peptide: Dyslexia-associated protein KIAA0319-like protein
    • Virus: Adeno-associated virus 9
      • Protein or peptide: Capsid protein VP1
KeywordsAdeno-associated virus serotype 9 / 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
Capsid protein VP1 / Dyslexia-associated protein KIAA0319-like protein
Similarity search - Component
Biological speciesHomo sapiens (human) / Adeno-associated virus 9
Methodsingle particle reconstruction / cryo EM / Resolution: 3.76 Å
AuthorsXu G / Lou Z
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mol Ther Methods Clin Dev / Year: 2022
Title: Structural basis for the neurotropic AAV9 and the engineered AAVPHP.eB recognition with cellular receptors.
Authors: Guangxue Xu / Ran Zhang / Huapeng Li / Kaixin Yin / Xinyi Ma / Zhiyong Lou /
Abstract: Clade F adeno-associated virus (AAV) 9 has been utilized as therapeutic gene delivery vector, and it is capable of crossing blood brain barrier (BBB). Recently, an AAV9-based engineering serotype ...Clade F adeno-associated virus (AAV) 9 has been utilized as therapeutic gene delivery vector, and it is capable of crossing blood brain barrier (BBB). Recently, an AAV9-based engineering serotype AAVPHP.eB with enhanced BBB crossing ability further expanded clade F AAVs' usages in the murine central nervous system (CNS) gene delivery. In this study, we determined the cryo-electron microscopy (cryo-EM) structures of the AAVPHP.eB and its parental serotype AAV9 in native form or in complex with their essential receptor AAV receptor (AAVR). These structures reveal the molecular details of their AAVR recognition, where the polycystic kidney disease repeat domain 2 (PKD2) of AAVR interacts with AAV9 and AAVPHP.eB virions at the 3-fold protrusions and the raised capsid regions between the 2- and 5-fold axes, termed the 2/5-fold wall. The interacting patterns of AAVR to AAV9 and AAVPHP.eB are similar to what was observed in AAV1/AAV2-AAVR complexes. Moreover, we found that the AAVPHP.eB variable region VIII (VR-VIII) may independently facilitate the new receptor recognition responsible for enhanced CNS transduction. Our study provides insights into the recognition principles of multiple receptors for engineered AAVPHP.eB and parental serotype AAV9, and further reveal the potential molecular basis underlying their different tropisms.
History
DepositionJan 25, 2022-
Header (metadata) releaseJun 15, 2022-
Map releaseJun 15, 2022-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32712.png

Downloads & links

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Map

FileDownload / File: emd_32712.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
Minimum - Maximum-0.12562647 - 0.19340841
Average (Standard dev.)0.0007737387 (±0.010722783)
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 °

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Supplemental data

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Sample components

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Entire : Adeno-associated virus 9

EntireName: Adeno-associated virus 9
Components
  • Complex: Adeno-associated virus 9
    • Complex: Dyslexia-associated protein KIAA0319-like protein
      • Protein or peptide: Dyslexia-associated protein KIAA0319-like protein
    • Virus: Adeno-associated virus 9
      • Protein or peptide: Capsid protein VP1

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Supramolecule #1: Adeno-associated virus 9

SupramoleculeName: Adeno-associated virus 9 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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

SupramoleculeName: Dyslexia-associated protein KIAA0319-like protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Adeno-associated virus 9

SupramoleculeName: Adeno-associated virus 9 / type: virus / ID: 3 / Parent: 1 / Macromolecule list: #2 / NCBI-ID: 235455 / Sci species name: Adeno-associated virus 9 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: Dyslexia-associated protein KIAA0319-like protein

MacromoleculeName: Dyslexia-associated protein KIAA0319-like protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.05609 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
NRPPIAIVSP QFQEISLPTT STVIDGSQST DDDKIVQYHW EELKGPLREE KISEDTAILK LSKLVPGNYT FSLTVVDSDG ATNSTTANL TVN

UniProtKB: Dyslexia-associated protein KIAA0319-like protein

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Macromolecule #2: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Adeno-associated virus 9
Molecular weightTheoretical: 59.205293 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DGVGSSSGNW HCDSQWLGDR VITTSTRTWA LPTYNNHLYK QISNSTSGGS SNDNAYFGYS TPWGYFDFNR FHCHFSPRDW QRLINNNWG FRPKRLNFKL FNIQVKEVTD NNGVKTIANN LTSTVQVFTD SDYQLPYVLG SAHEGCLPPF PADVFMIPQY G YLTLNDGS ...String:
DGVGSSSGNW HCDSQWLGDR VITTSTRTWA LPTYNNHLYK QISNSTSGGS SNDNAYFGYS TPWGYFDFNR FHCHFSPRDW QRLINNNWG FRPKRLNFKL FNIQVKEVTD NNGVKTIANN LTSTVQVFTD SDYQLPYVLG SAHEGCLPPF PADVFMIPQY G YLTLNDGS QAVGRSSFYC LEYFPSQMLR TGNNFQFSYE FENVPFHSSY AHSQSLDRLM NPLIDQYLYY LSKTINGSGQ NQ QTLKFSV AGPSNMAVQG RNYIPGPSYR QQRVSTTVTQ NNNSEFAWPG ASSWALNGRN SLMNPGPAMA SHKEGEDRFF PLS GSLIFG KQGTGRDNVD ADKVMITNEE EIKTTNPVAT ESYGQVATNH QSDGTLAVPF KAQAQTGWVQ NQGILPGMVW QDRD VYLQG PIWAKIPHTD GNFHPSPLMG GFGMKHPPPQ ILIKNTPVPA DPPTAFNKDK LNSFITQYST GQVSVEIEWE LQKEN SKRW NPEIQYTSNY YKSNNVEFAV NTEGVYSEPR PIGTRYLTRN L

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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 35.7 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
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
PDB model - PDB ID:

3ux1

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 16526
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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