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- EMDB-61206: Structure of AAV8 capsid in complex with receptor -

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Basic information

Entry
Database: EMDB / ID: EMD-61206
TitleStructure of AAV8 capsid in complex with receptor
Map data
Sample
  • Complex: Complex of AAV8 with receptor
    • Protein or peptide: Capsid protein
    • Protein or peptide: Carboxypeptidase D
Keywordsreceptor / AAV8 / 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 / Peptidase family M14 domain profile. / Zinc carboxypeptidase ...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 / Peptidase family M14 domain profile. / Zinc carboxypeptidase / 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 speciesHomo sapiens (human) / Adeno-associated virus - 8
Methodsingle particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsXu H / Wang GP / Su XD
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: Cell / Year: 2025
Title: Structure of AAV8 in complex with its receptor
Authors: Xu H / Wang GP / Su XD
History
DepositionAug 19, 2024-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61206.png

Downloads & links

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Map

FileDownload / File: emd_61206.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

Slices (1/3)

Slices (1/2)

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-0.042245854 - 0.103455074
Average (Standard dev.)0.00074689393 (±0.005483903)
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_61206_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_61206_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of AAV8 with receptor

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

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Supramolecule #1: Complex of AAV8 with receptor

SupramoleculeName: Complex of AAV8 with receptor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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: 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: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 43040
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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