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- EMDB-10325: cryo-EM map of ASFV MCP p72 homotrimers purified from virion -

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Basic information

Entry
Database: EMDB / ID: EMD-10325
Titlecryo-EM map of ASFV MCP p72 homotrimers purified from virion
Map dataP72 postprocess map
Sample
  • Complex: homotrimer of Major Capsid Protein p72 of African Swine Fever virus
    • Protein or peptide: viral major capsid protein p72
Biological speciesAfrican swine fever virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsAbrescia NG / Andres G / Charro D
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 22, 2019-
Header (metadata) releaseNov 6, 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: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10325.png

Downloads & links

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Map

FileDownload / File: emd_10325.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationP72 postprocess map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 192 pix.
= 216.96 Å		1.13 Å/pix.
x 192 pix.
= 216.96 Å		1.13 Å/pix.
x 192 pix.
= 216.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.13 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.033545695 - 0.06106012
Average (Standard dev.)0.00023992131 (±0.003953747)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 216.95999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.131.131.13
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z216.960216.960216.960
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.0340.0610.000

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Supplemental data

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Mask #1

Fileemd_10325_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: local resolution filtered map

Fileemd_10325_additional_1.map
Annotationlocal resolution filtered map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: for coloring locres

Fileemd_10325_additional_2.map
Annotationfor coloring locres
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: P72 Half1

Fileemd_10325_half_map_1.map
AnnotationP72 Half1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: P72 Half2

Fileemd_10325_half_map_2.map
AnnotationP72 Half2
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : homotrimer of Major Capsid Protein p72 of African Swine Fever virus

EntireName: homotrimer of Major Capsid Protein p72 of African Swine Fever virus
Components
  • Complex: homotrimer of Major Capsid Protein p72 of African Swine Fever virus
    • Protein or peptide: viral major capsid protein p72

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Supramolecule #1: homotrimer of Major Capsid Protein p72 of African Swine Fever virus

SupramoleculeName: homotrimer of Major Capsid Protein p72 of African Swine Fever virus
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: purified from virion
Source (natural)Organism: African swine fever virus / Strain: Ba71V

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Macromolecule #1: viral major capsid protein p72

MacromoleculeName: viral major capsid protein p72 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: African swine fever virus / Strain: strain Badajoz 1971
SequenceString: MASGGAFCLI ANDGKADKII LAQDLLNSRI SNIKNVNKSY GKPDPEPTLS QIEETHLVHF NAHFKPYVP VGFEYNKVRP HTGTPTLGNK LTFGIPQYGD FFHDMVGHHI LGACHSSWQD A PIQGTAQM GAHGQLQTFP RNGYDWDNQT PLEGAVYTLV DPFGRPIVPG ...String:
MASGGAFCLI ANDGKADKII LAQDLLNSRI SNIKNVNKSY GKPDPEPTLS QIEETHLVHF NAHFKPYVP VGFEYNKVRP HTGTPTLGNK LTFGIPQYGD FFHDMVGHHI LGACHSSWQD A PIQGTAQM GAHGQLQTFP RNGYDWDNQT PLEGAVYTLV DPFGRPIVPG TKNAYRNLVY YC EYPGERL YENVRFDVNG NSLDEYSSDV TTLVRKFCIP GDKMTGYKHL VGQEVSVEGT SGP LLCNIH DLHKPHQSKP ILTDENDTQR TCSHTNPKFL SQHFPENSHN IQTAGKQDIT PITD ATYLD IRRNVHYSCN GPQTPKYYQP PLALWIKLRF WFNENVNLAI PSVSIPFGER FITIK LASQ KDLVNEFPGL FIRQSRFIPG RPSRRNIRFK PWFIPGVINE ISLTNNELYI NNLFVT PEI HNLFVKRVRF SLIRVHKTQV THTNNNHHDE KLMSALKWPI EYMFIGLKPT WNISDQN PH QHRDWHKFGH VVNAIMQPTH HAEISFQDRD TALPDACSSI SDISPVTYPI TLPIIKNI S VTAHGINLID KFPSKFCSSY IPFHYGGNAI KTPDDPGAMM ITFALKPREE YQPSGHINV SRAREFYISW DTDYVGSITT ADLVVSASAI NFLLLQNGSA VLRYST

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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 - Name: PBS
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1541 / Average electron dose: 46.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Cs: 0.01 mm / Nominal magnification: 59000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2710425
CTF correctionSoftware - Name: CTFFIND
Startup modelType of model: INSILICO MODEL / In silico model: Generated with Relion
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 337803
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
FSC plot (resolution estimation)

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