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- EMDB-61205: Structure of AAV8 in the complex of AAV8 with its receptor -

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Basic information

Entry
Database: EMDB / ID: EMD-61205
TitleStructure of AAV8 in the complex of AAV8 with its receptor
Map data
Sample
  • Virus: adeno-associated virus 8
    • Protein or peptide: Capsid protein
KeywordsAAV8 / virus / complex
Function / homology
Function and homology information


T=1 icosahedral viral capsid / nucleotide binding / 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 VP2 / Capsid/spike protein, ssDNA virus
Similarity search - Domain/homology
Biological speciesAdeno-associated virus - 8 / adeno-associated virus 8
Methodsingle particle reconstruction / cryo EM / Resolution: 2.32 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: 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_61205.png

Downloads & links

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Map

FileDownload / File: emd_61205.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 460 pix.
= 492.2 Å		1.07 Å/pix.
x 460 pix.
= 492.2 Å		1.07 Å/pix.
x 460 pix.
= 492.2 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: 0.04
Minimum - Maximum-0.13883547 - 0.26634085
Average (Standard dev.)0.00075661816 (±0.010859941)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 492.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_61205_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_61205_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 : adeno-associated virus 8

EntireName: adeno-associated virus 8
Components
  • Virus: adeno-associated virus 8
    • Protein or peptide: Capsid protein

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Supramolecule #1: adeno-associated virus 8

SupramoleculeName: adeno-associated virus 8 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 202813 / Sci species name: adeno-associated virus 8 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 60 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.8 mg/mL
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: 2.32 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 235305
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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