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- EMDB-61190: Structure of AAV8 in complex with its receptor -

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Basic information

Entry
Database: EMDB / ID: EMD-61190
TitleStructure of AAV8 in complex with its receptor
Map data
Sample
  • Complex: AAV8 in complex with receptor
    • Protein or peptide: Capsid protein
    • Protein or peptide: Carboxypeptidase D
KeywordsAAV8 / receptor / complex / VIRAL PROTEIN/HYDROLASE / VIRAL PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


metallocarboxypeptidase D / serine-type carboxypeptidase activity / peptide metabolic process / RND1 GTPase cycle / RND3 GTPase cycle / T=1 icosahedral viral capsid / Golgi Associated Vesicle Biogenesis / metallocarboxypeptidase activity / protein processing / nucleotide binding ...metallocarboxypeptidase D / serine-type carboxypeptidase activity / peptide metabolic process / RND1 GTPase cycle / RND3 GTPase cycle / T=1 icosahedral viral capsid / Golgi Associated Vesicle Biogenesis / metallocarboxypeptidase activity / protein processing / nucleotide binding / structural molecule activity / extracellular space / extracellular exosome / zinc ion binding / membrane / plasma membrane
Similarity search - Function
Carboxypeptidase D, carboxypeptidase-like domain 3 / Carboxypeptidase D, carboxypeptidase-like domain 2 / : / Carboxypeptidase regulatory-like domain / Carboxypeptidase-like, regulatory domain superfamily / Zinc carboxypeptidases, zinc-binding region 2 signature. / Zinc carboxypeptidases, zinc-binding region 1 signature. / Zn_pept / Zinc carboxypeptidase / Peptidase family M14 domain profile. ...Carboxypeptidase D, carboxypeptidase-like domain 3 / Carboxypeptidase D, carboxypeptidase-like domain 2 / : / Carboxypeptidase regulatory-like domain / Carboxypeptidase-like, regulatory domain superfamily / Zinc carboxypeptidases, zinc-binding region 2 signature. / Zinc carboxypeptidases, zinc-binding region 1 signature. / Zn_pept / Zinc carboxypeptidase / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A / Phospholipase A2-like domain / Phospholipase A2-like domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus
Similarity search - Domain/homology
Carboxypeptidase D / Capsid protein
Similarity search - Component
Biological speciesAdeno-associated virus - 8 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsXu H / Wang GP / Su XD
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFC2301402 China
CitationJournal: Cell / Year: 2025
Title: An alternate receptor for adeno-associated viruses.
Authors: Bijay P Dhungel / Hua Xu / Rajini Nagarajah / Joseph Vitale / Alex C H Wong / Divya Gokal / Yue Feng / Mehdi Sharifi Tabar / Cynthia Metierre / Chirag Parsania / Xiaohui Song / Guopeng Wang ...Authors: Bijay P Dhungel / Hua Xu / Rajini Nagarajah / Joseph Vitale / Alex C H Wong / Divya Gokal / Yue Feng / Mehdi Sharifi Tabar / Cynthia Metierre / Chirag Parsania / Xiaohui Song / Guopeng Wang / Xiao-Dong Su / Charles G Bailey / John E J Rasko /
Abstract: Systemic gene therapy using adeno-associated virus (AAV) vectors is approved for the treatment of several genetic disorders, but challenges and toxicities associated with high vector doses remain. We ...Systemic gene therapy using adeno-associated virus (AAV) vectors is approved for the treatment of several genetic disorders, but challenges and toxicities associated with high vector doses remain. We report an alternate receptor for AAV (AAVR2, carboxypeptidase D [CPD]), which is distinct from the multi-serotype AAV receptor (AAVR). AAVR2 enables the transduction of clade E AAVs, including AAV8, and determines an exclusive AAVR-independent transduction pathway for AAV11 and AAV12. We characterized direct binding between the AAV8 capsid and AAVR2 by cryo-electron microscopy (cryo-EM) and identified contact residues. We observed that AAV8 directly binds to the carboxypeptidase-like domain 1 of AAVR2 via its variable region VIII and demonstrated that AAV capsids that lack AAVR2 binding can be bioengineered to engage with AAVR2. Finally, we overexpressed a minimal functional AAVR2 to enhance AAV transduction in vivo. Our study provides insights into AAV biology and clinically deployable solutions to reduce dose-related toxicities associated with AAV vectors.
History
DepositionAug 17, 2024-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61190.png

Downloads & links

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Map

FileDownload / File: emd_61190.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 192 pix.
= 205.44 Å		1.07 Å/pix.
x 192 pix.
= 205.44 Å		1.07 Å/pix.
x 192 pix.
= 205.44 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.040721547 - 0.09501169
Average (Standard dev.)0.00074967276 (±0.0052806307)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 205.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_61190_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61190_half_map_2.map
Projections & Slices
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Sample components

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Entire : AAV8 in complex with receptor

EntireName: AAV8 in complex with receptor
Components
  • Complex: AAV8 in complex with receptor
    • Protein or peptide: Capsid protein
    • Protein or peptide: Carboxypeptidase D

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Supramolecule #1: AAV8 in complex with receptor

SupramoleculeName: AAV8 in complex with receptor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Adeno-associated virus - 8

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Adeno-associated virus - 8
Molecular weightTheoretical: 81.833047 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAADGYLPDW LEDNLSEGIR EWWALKPGAP KPKANQQKQD DGRGLVLPGY KYLGPFNGLD KGEPVNAADA AALEHDKAYD QQLQAGDNP YLRYNHADAE FQERLQEDTS FGGNLGRAVF QAKKRVLEPL GLVEEGAKTA PGKKRPVEPS PQRSPDSSTG I GKKGQQPA ...String:
MAADGYLPDW LEDNLSEGIR EWWALKPGAP KPKANQQKQD DGRGLVLPGY KYLGPFNGLD KGEPVNAADA AALEHDKAYD QQLQAGDNP YLRYNHADAE FQERLQEDTS FGGNLGRAVF QAKKRVLEPL GLVEEGAKTA PGKKRPVEPS PQRSPDSSTG I GKKGQQPA RKRLNFGQTG DSESVPDPQP LGEPPAAPSG VGPNTMAAGG GAPMADNNEG ADGVGSSSGN WHCDSTWLGD RV ITTSTRT WALPTYNNHL YKQISNGTSG GATNDNTYFG YSTPWGYFDF NRFHCHFSPR DWQRLINNNW GFRPKRLSFK LFN IQVKEV TQNEGTKTIA NNLTSTIQVF TDSEYQLPYV LGSAHQGCLP PFPADVFMIP QYGYLTLNNG SQAVGRSSFY CLEY FPSQM LRTGNNFQFT YTFEDVPFHS SYAHSQSLDR LMNPLIDQYL YYLSRTQTTG GTANTQTLGF SQGGPNTMAN QAKNW LPGP CYRQQRVSTT TGQNNNSNFA WTAGTKYHLN GRNSLANPGI AMATHKDDEE RFFPSNGILI FGKQNAARDN ADYSDV MLT SEEEIKTTNP VATEEYGIVA DNLQQQNTAP QIGTVNSQGA LPGMVWQNRD VYLQGPIWAK IPHTDGNFHP SPLMGGF GL KHPPPQILIK NTPVPADPPT TFNQSKLNSF ITQYSTGQVS VEIEWELQKE NSKRWNPEIQ YTSNYYKSTS VDFAVNTE G VYSEPRPIGT RYLTRNL

UniProtKB: Capsid protein

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Macromolecule #2: Carboxypeptidase D

MacromoleculeName: Carboxypeptidase D / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: metallocarboxypeptidase D
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.9855 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AHIKKAEATT TTTSAGAEAA EGQFDRYYHE EELESALREA AAAGLPGLAR LFSIGRSVEG RPLWVLRLTA GLGSLIPEGD AGPDAAGPD AAGPLLPGRP QVKLVGNMHG DETVSRQVLI YLARELAAGY RRGDPRLVRL LNTTDVYLLP SLNPDGFERA R EGDCGFGD ...String:
AHIKKAEATT TTTSAGAEAA EGQFDRYYHE EELESALREA AAAGLPGLAR LFSIGRSVEG RPLWVLRLTA GLGSLIPEGD AGPDAAGPD AAGPLLPGRP QVKLVGNMHG DETVSRQVLI YLARELAAGY RRGDPRLVRL LNTTDVYLLP SLNPDGFERA R EGDCGFGD GGPSGASGRD NSRGRDLNRS FPDQFSTGEP PALDEVPEVR ALIEWIRRNK FVLSGNLHGG SVVASYPFDD SP EHKATGI YSKTSDDEVF KYLAKAYASN HPIMKTGEPH CPGDEDETFK DGITNGAHWY DVEGGMQDYN YVWANCFEIT LEL SCCKYP PASQLRQEWE NNRESLITLI EKVHIGVKGF VKDSITGSGL ENATISVAGI NHNITTGRFG DFYRLLVPGT YNLT VVLTG YMPLTVTNVV VKEGPATEVD FSLRPTVTSV IPDTTEAVST ASTVAIPNIL SGTSSSYHHH HHHHH

UniProtKB: Carboxypeptidase D

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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: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30953
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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