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- EMDB-63323: Structure of bovine adenovirus type 3 capsid -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-63323
TitleStructure of bovine adenovirus type 3 capsid
Map data
Sample
  • Virus: Bovine adenovirus 3
KeywordsComplex / VIRUS
Biological speciesBovine adenovirus 3
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsXiao H / Liu HR
Funding support China, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32430020 China
National Natural Science Foundation of China (NSFC)32371263 China
National Natural Science Foundation of China (NSFC)32401014 China
CitationJournal: J Mol Biol / Year: 2025
Title: Structural Insights into Minor and Core Proteins of Bovine Adenovirus 3: Bridging Capsid and Genomic Core.
Authors: Hao Xiao / Hao Pang / Junquan Zhou / Hao Feng / Jingdong Song / Lingpeng Cheng / Li Wang / Hongrong Liu /
Abstract: Adenoviruses are double-stranded DNA viruses with broad relevance to human and animal health and considerable potential as therapeutic vectors. Despite extensive studies, the structural details of ...Adenoviruses are double-stranded DNA viruses with broad relevance to human and animal health and considerable potential as therapeutic vectors. Despite extensive studies, the structural details of core and minor capsid proteins in adenoviruses remain poorly understood. In this study, the architecture of bovine adenovirus type 3 (BAdV-3), a member of the Mastadenovirus genus, was solved by cryo-electron microscopy. Our structure shows that BAdV-3 shares significant structural conservation with human adenoviruses. Atomic models were constructed for a previously uncharacterized region of the minor protein VI and for the core proteins V and Mu. The study revealed how core proteins bridge the genome and capsid, underscore the multifaceted roles of protein V in strengthening capsid stability and facilitating genome release.
History
DepositionJan 30, 2025-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63323.png

Downloads & links

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Map

FileDownload / File: emd_63323.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.27 Å/pix.
x 800 pix.
= 1016. Å		1.27 Å/pix.
x 800 pix.
= 1016. Å		1.27 Å/pix.
x 800 pix.
= 1016. Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.27 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 15.0
Minimum - Maximum-37.72889 - 76.110699999999994
Average (Standard dev.)0.5035057 (±6.1996408)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-400-400-400
Dimensions800800800
Spacing800800800
CellA=B=C: 1016.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63323_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_63323_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Bovine adenovirus 3

EntireName: Bovine adenovirus 3
Components
  • Virus: Bovine adenovirus 3

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Supramolecule #1: Bovine adenovirus 3

SupramoleculeName: Bovine adenovirus 3 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10510 / Sci species name: Bovine adenovirus 3 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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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 TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.6 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 45000
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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