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- EMDB-64272: Structure of Modified adeno-associated viral vector, AAV5-BCD -

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Basic information

Entry
Database: EMDB / ID: EMD-64272
TitleStructure of Modified adeno-associated viral vector, AAV5-BCD
Map data
Sample
  • Virus: adeno-associated virus 5
    • Protein or peptide: Capsid protein
Keywordsadeno-associated virus / AAV5 / VIRUS
Function / homologyPhospholipase 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 / T=1 icosahedral viral capsid / structural molecule activity / Capsid protein
Function and homology information
Biological speciesadeno-associated virus 5
Methodsingle particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsZhang H / Burtseva AD / Strelkova AN / Perepelkina MP / Iurlova EV / Gershovich PM / Prokof'ev AV / Kolesnichenko AS / Gulnova AR / Nurtdinov RF ...Zhang H / Burtseva AD / Strelkova AN / Perepelkina MP / Iurlova EV / Gershovich PM / Prokof'ev AV / Kolesnichenko AS / Gulnova AR / Nurtdinov RF / Vasilev AA / Yakovlev PA / Popov VO / Boyko KM
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of Modified adeno-associated viral vector, AAV5-BCD
Authors: Zhang H / Burtseva A / Boyko K
History
DepositionApr 21, 2025-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64272.png

Downloads & links

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Map

FileDownload / File: emd_64272.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 480 pix.
= 410.4 Å		0.86 Å/pix.
x 480 pix.
= 410.4 Å		0.86 Å/pix.
x 480 pix.
= 410.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-5.4355946 - 8.156966000000001
Average (Standard dev.)0.009843235 (±0.45239776)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 410.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64272_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64272_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 5

EntireName: adeno-associated virus 5
Components
  • Virus: adeno-associated virus 5
    • Protein or peptide: Capsid protein

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Supramolecule #1: adeno-associated virus 5

SupramoleculeName: adeno-associated virus 5 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 82300 / Sci species name: adeno-associated virus 5 / Virus type: VIRUS-LIKE PARTICLE / 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 5
Molecular weightTheoretical: 80.467391 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAFVDHPPDW LEEVGEGLRE FLGLEAGPPK PKPNQQHQDQ ARGLVLPGYN YLGPGNGLDR GEPVNRADEV AREHDISYNE QLEAGDNPY LKYNHADAEF QEKLADDTSF GGNLGKAVFQ AKKRVLEPFG LVEEGAKTAP TGKRIDDHFP KRKKARTEED S KPSTSSDA ...String:
MAFVDHPPDW LEEVGEGLRE FLGLEAGPPK PKPNQQHQDQ ARGLVLPGYN YLGPGNGLDR GEPVNRADEV AREHDISYNE QLEAGDNPY LKYNHADAEF QEKLADDTSF GGNLGKAVFQ AKKRVLEPFG LVEEGAKTAP TGKRIDDHFP KRKKARTEED S KPSTSSDA EAGPSGSQQL QIPAQPASSL GADTMSAGGG GPLGDNNQGA DGVGNASGDW HCDSTWMGDR VVTKSTRTWV LP SYNNHQY REIKSGSVDG SNANAYFGYS TPWGYFDFNR FHSHWSPRDW QRLINNYWGF RPRSLRVKIF NIQVKEVTVQ DST TTIANN LTSTVQVFTD DDYQLPYVVG NGTEGCLPAF PPQVFTLPQY GYATLNRDNT ENPTERSSFF CLEYFPSKML RTGN NFEFT YNFEEVPFHS SFAPSQNLFK LANPLVDQYL YRFVSTNNTG GVQFNKNLAG RYANTYKNWF PGPMGRTQGW NLGSG VNRA SVSAFATTNR MELEGASYQV PPQPNGMTNN LQGSNTYALE NTMIFNSQPA NPGTTATYLE GNMLITSESE TQPVNR VAY NVGGQMATNN QSSTTAPATG TYNLQEIVPG SVWMERDVYL QGPIWAKIPE TGAHFHPSPA MGGFGLKHPP PMMLIKN TP VPGNITSFSD VPVSSFITQY STGQVTVEME WELKKENSKR WNPEIQYTNN YNDPQFVDFA PDSTGEYRST RPIGTRYL T RPL

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

BufferpH: 8.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.0 µm / Calibrated defocus min: 1.0 µm / Illumination 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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 285362
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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