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- EMDB-19396: FAdV-C4 AG234 Aviadenovirus structure, strain AG234 -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-19396
TitleFAdV-C4 AG234 Aviadenovirus structure, strain AG234
Map data
Sample
  • Virus: Fowl aviadenovirus 4
Keywordsadenovirus / fowl / highly thermostable / VIRUS
Biological speciesFowl aviadenovirus 4
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsPerez-Illana MP / Schachnner A / Condezo GN / Hernando-Perez M / Martinez M / Marabini R / Hess M / San Martin C
Funding support2 items
OrganizationGrant numberCountry
Other privateLa Caixa Foundation (ID 100010434),La Caixa Foundation (ID 100010434),LCF/BQ/SO16/52270032)
Other governmentco-funded by the Spanish State Research Agency and the European Regional Development Fund, PID2022-136456NB-I00/ AEI/10.13039/501100011033/FEDER,UE
CitationJournal: To Be Published
Title: FAdV-C4 AG234 Aviadenovirus structure, strain AG234
Authors: Perez-Illana MP / Schachnner A / Condezo GN / Hernando-Perez M / Martinez M / Marabini R / Hess M / San Martin C
History
DepositionJan 11, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateJan 29, 2025-
Current statusJan 29, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19396.png

Downloads & links

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Map

FileDownload / File: emd_19396.map.gz / Format: CCP4 / Size: 1.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.38 Å/pix.
x 752 pix.
= 1034. Å		1.38 Å/pix.
x 752 pix.
= 1034. Å		1.38 Å/pix.
x 752 pix.
= 1034. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.375 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.055
Minimum - Maximum-0.12381991 - 0.21060576
Average (Standard dev.)0.00063285825 (±0.016218984)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-376-376-376
Dimensions752752752
Spacing752752752
CellA=B=C: 1034.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_19396_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_19396_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 : Fowl aviadenovirus 4

EntireName: Fowl aviadenovirus 4
Components
  • Virus: Fowl aviadenovirus 4

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Supramolecule #1: Fowl aviadenovirus 4

SupramoleculeName: Fowl aviadenovirus 4 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 130663 / Sci species name: Fowl aviadenovirus 4 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Gallus gallus (chicken)

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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: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 97902 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 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: OTHER
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 40383
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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