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- EMDB-17321: Cryotomogram of Prototype Foamy Virus particles, wild-type Gag -

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Basic information

Entry
Database: EMDB / ID: EMD-17321
TitleCryotomogram of Prototype Foamy Virus particles, wild-type Gag
Map data
Sample
  • Virus: Eastern chimpanzee simian foamy virus
Keywordscapsid / Gag / full-length / CA domain / VIRAL PROTEIN
Biological speciesEastern chimpanzee simian foamy virus
Methodelectron tomography / cryo EM
AuthorsCalcraft T / Nans A / Rosenthal PB
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
The Francis Crick Institute United Kingdom
CitationJournal: Cell / Year: 2024
Title: Integrated cryoEM structure of a spumaretrovirus reveals cross-kingdom evolutionary relationships and the molecular basis for assembly and virus entry.
Authors: Thomas Calcraft / Nicole Stanke-Scheffler / Andrea Nans / Dirk Lindemann / Ian A Taylor / Peter B Rosenthal /
Abstract: Foamy viruses (FVs) are an ancient lineage of retroviruses, with an evolutionary history spanning over 450 million years. Vector systems based on Prototype Foamy Virus (PFV) are promising candidates ...Foamy viruses (FVs) are an ancient lineage of retroviruses, with an evolutionary history spanning over 450 million years. Vector systems based on Prototype Foamy Virus (PFV) are promising candidates for gene and oncolytic therapies. Structural studies of PFV contribute to the understanding of the mechanisms of FV replication, cell entry and infection, and retroviral evolution. Here we combine cryoEM and cryoET to determine high-resolution in situ structures of the PFV icosahedral capsid (CA) and envelope glycoprotein (Env), including its type III transmembrane anchor and membrane-proximal external region (MPER), and show how they are organized in an integrated structure of assembled PFV particles. The atomic models reveal an ancient retroviral capsid architecture and an unexpected relationship between Env and other class 1 fusion proteins of the Mononegavirales. Our results represent the de novo structure determination of an assembled retrovirus particle.
History
DepositionMay 9, 2023-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateAug 21, 2024-
Current statusAug 21, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17321.png

Downloads & links

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Map

FileDownload / File: emd_17321.map.gz / Format: CCP4 / Size: 1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.52 Å/pix.
x 312 pix.
= 1722.24 Å		5.52 Å/pix.
x 927 pix.
= 5117.04 Å		5.52 Å/pix.
x 959 pix.
= 5293.68 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 5.52 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-26.535278000000002 - 16.141909999999999
Average (Standard dev.)0.50240403 (±0.68036973)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-312
Dimensions927959312
Spacing959927312
CellA: 5293.68 Å / B: 5117.04 Å / C: 1722.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Eastern chimpanzee simian foamy virus

EntireName: Eastern chimpanzee simian foamy virus
Components
  • Virus: Eastern chimpanzee simian foamy virus

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Supramolecule #1: Eastern chimpanzee simian foamy virus

SupramoleculeName: Eastern chimpanzee simian foamy virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 2170195 / Sci species name: Eastern chimpanzee simian foamy virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Virus shellShell ID: 1 / T number (triangulation number): 13

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK III
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: BBI Solutions / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Average electron dose: 2.62 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 2.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION
Software:
Namedetails
NOVACTFCTF correction and reconstruction
Bsoft

Number images used: 41

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