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- EMDB-32572: African swine fever virus major capsid protein p72 trimer -

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Basic information

Entry
Database: EMDB / ID: EMD-32572
TitleAfrican swine fever virus major capsid protein p72 trimer
Map data
Sample
  • Complex: African swine fever virus major capsid protein p72 trimer
Biological speciesAfrican swine fever virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.18 Å
AuthorsLiu Q
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Front Microbiol / Year: 2022
Title: Structural Design and Assessing of Recombinantly Expressed African Swine Fever Virus p72 Trimer in .
Authors: Kaiwen Meng / Yueping Zhang / Qi Liu / Yangnan Huyan / Wenzhuang Zhu / Ye Xiang / Geng Meng /
Abstract: In an effort to control the outbreak of the African Swine Fever Virus (ASFV), there is an urgent need to develop an effective method to prevent the pandemic, including vaccines and diagnostic methods. ...In an effort to control the outbreak of the African Swine Fever Virus (ASFV), there is an urgent need to develop an effective method to prevent the pandemic, including vaccines and diagnostic methods. The major capsid protein of ASFV p72 (B646L), which forms a trimer with each monomer adopting a double jelly roll fold, is the main component of the virus particle and major antigen of ASFV. Thus, the p72 protein may be considered an antigen candidate for vaccine and diagnostic development. However, the development of ASFV p72 trimer for the industry application, including veterinary usage, faces unavoidable challenges: firstly, the low cost of the antigen production is required in vaccine and diagnostic application; and, secondly, whether produced antigen folds in its native conformation. Here, based on the information provided by the atomic structure of p72, we have successfully performed rational mutagenesis on p72 trimers and expressed it in with high yields. The cryo-EM structure of recombinant expressed p72 trimer is determined at 4.18 Å in resolution. The correlation coefficient between this structure and the ASFV virus structure is 0.77, suggesting a highly similar fold of this trimer with the native protein on the virus particle.
History
DepositionJan 12, 2022-
Header (metadata) releaseDec 21, 2022-
Map releaseDec 21, 2022-
UpdateDec 21, 2022-
Current statusDec 21, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32572.png

Downloads & links

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Map

FileDownload / File: emd_32572.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 240 pix.
= 263.496 Å		1.1 Å/pix.
x 240 pix.
= 263.496 Å		1.1 Å/pix.
x 240 pix.
= 263.496 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0979 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0112
Minimum - Maximum-0.0060200454 - 0.025551843
Average (Standard dev.)0.00013413238 (±0.0014083997)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 263.496 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : African swine fever virus major capsid protein p72 trimer

EntireName: African swine fever virus major capsid protein p72 trimer
Components
  • Complex: African swine fever virus major capsid protein p72 trimer

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Supramolecule #1: African swine fever virus major capsid protein p72 trimer

SupramoleculeName: African swine fever virus major capsid protein p72 trimer
type: complex / Chimera: Yes / ID: 1 / Parent: 0
Source (natural)Organism: African swine fever virus

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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

Concentration0.25 mg/mL
BufferpH: 7.4
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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ball as the initial model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 143740
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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