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- EMDB-10346: Structure of African Swine fever virus -

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Basic information

Entry
Database: EMDB / ID: EMD-10346
TitleStructure of African Swine fever virus
Map dataPostprocessed map
Sample
  • Virus: African swine fever virus BA71V
Biological speciesAfrican swine fever virus BA71V
Methodsingle particle reconstruction / cryo EM / Resolution: 23.1 Å
AuthorsAbrescia NG / Andres G / Charro D / Matamoros T / Dillard R
Funding support Spain, 3 items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPGC2018-098701-B-I00 Spain
Spanish Ministry of Economy and CompetitivenessSEV-2016-0644 Spain
Spanish Ministry of Science, Innovation, and UniversitiesRTI2018-095700-B-I00 Spain
CitationJournal: J Biol Chem / Year: 2020
Title: The cryo-EM structure of African swine fever virus unravels a unique architecture comprising two icosahedral protein capsids and two lipoprotein membranes.
Authors: German Andrés / Diego Charro / Tania Matamoros / Rebecca S Dillard / Nicola G A Abrescia /
Abstract: African swine fever virus (ASFV) is a complex nucleocytoplasmic large DNA virus (NCLDV) that causes a devastating swine disease currently present in many countries of Africa, Europe, and Asia. ...African swine fever virus (ASFV) is a complex nucleocytoplasmic large DNA virus (NCLDV) that causes a devastating swine disease currently present in many countries of Africa, Europe, and Asia. Despite intense research efforts, relevant gaps in the architecture of the infectious virus particle remain. Here, we used single-particle cryo-EM to analyze the three-dimensional structure of the mature ASFV particle. Our results show that the ASFV virion, with a radial diameter of ∼2,080 Å, encloses a genome-containing nucleoid surrounded by two distinct icosahedral protein capsids and two lipoprotein membranes. The outer capsid forms a hexagonal lattice (triangulation number = 277) composed of 8,280 copies of the double jelly-roll major capsid protein (MCP) p72, arranged in trimers displaying a pseudo-hexameric morphology, and of 60 copies of a penton protein at the vertices. The inner protein layer, organized as a = 19 capsid, confines the core shell, and it is composed of the mature products derived from the ASFV polyproteins pp220 and pp62. Also, an icosahedral membrane lies between the two protein layers, whereas a pleomorphic envelope wraps the outer capsid. This high-level organization confers to ASFV a unique architecture among the NCLDVs that likely reflects the complexity of its infection process and may help explain current challenges in controlling it.
History
DepositionSep 26, 2019-
Header (metadata) releaseOct 30, 2019-
Map releaseNov 6, 2019-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.028
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10346.png

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Map

FileDownload / File: emd_10346.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
2.94 Å/pix.
x 1000 pix.
= 2938. Å		2.94 Å/pix.
x 1000 pix.
= 2938. Å		2.94 Å/pix.
x 1000 pix.
= 2938. Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.938 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.028 / Movie #1: 0.028
Minimum - Maximum-0.07193008 - 0.51178
Average (Standard dev.)-0.0000000000 (±0.022948122)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100010001000
Spacing100010001000
CellA=B=C: 2938.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.9382.9382.938
M x/y/z100010001000
origin x/y/z0.0000.0000.000
length x/y/z2938.0002938.0002938.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100010001000
D min/max/mean-0.0720.512-0.000

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Supplemental data

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Mask #1

Fileemd_10346_msk_1.map
Projections & Slices
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Additional map: nucleocapsid

Fileemd_10346_additional_1.map
Annotationnucleocapsid
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Additional map: simmetrized nucleocapsid

Fileemd_10346_additional_2.map
Annotationsimmetrized nucleocapsid
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Half map: Half 2

Fileemd_10346_half_map_1.map
AnnotationHalf 2
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Half map: Half 1

Fileemd_10346_half_map_2.map
AnnotationHalf 1
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Sample components

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Entire : African swine fever virus BA71V

EntireName: African swine fever virus BA71V
Components
  • Virus: African swine fever virus BA71V

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Supramolecule #1: African swine fever virus BA71V

SupramoleculeName: African swine fever virus BA71V / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 10498 / Sci species name: African swine fever virus BA71V / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: pigs, warthogs, bushpigs (unknown)
Virus shellShell ID: 1 / Name: Outer capsid (MCP p72) / Diameter: 2400.0 Å / T number (triangulation number): 277

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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

Concentration1.1 mg/mL
BufferpH: 7.4 / Component - Formula: PBS
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DetailsTwo datasets were acquired.
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: FEI FALCON III (4k x 4k) / #0 - Average electron dose: 47.7 e/Å2
#0 - Details: Titan Krios equipped with a Cs-corrector and a Falcon 3EC direct electron detector
#1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #1 - Average electron dose: 47.5 e/Å2
#1 - Details: Titan Krios equipped with a Gatan K2 Summit direct electron detector
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID2
Particle selectionNumber selected: 1267
Details: 583 from Falcon 3EC dataset plus 684 from K2 dataset
CTF correctionSoftware - Name: CTFFIND
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 23.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 1110
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 2 / Software - Name: RELION
Details: From the first data collection 583 ASFV particles were visually selected and extracted in RELION, and 3D classified in two classes (as a reference an initial symmetrized model was generated ...Details: From the first data collection 583 ASFV particles were visually selected and extracted in RELION, and 3D classified in two classes (as a reference an initial symmetrized model was generated in RELION). The largest class with 450 particles was refined and a preliminary icosahedral model of the virion was produced; this model served as reference for the 3D classification of the second dataset (684 starting particles) which led to a largest class with 650 particles. Then both set of particles were interpolated to the same pixel size and merged for 3D reconstruction.
FSC plot (resolution estimation)

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