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- EMDB-17313: In situ cryoEM structure of the Prototype Foamy Virus capsid, pen... -

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Basic information

Entry
Database: EMDB / ID: EMD-17313
TitleIn situ cryoEM structure of the Prototype Foamy Virus capsid, pentamer localised reconstruction
Map data
Sample
  • Virus: Eastern chimpanzee simian foamy virus
    • Protein or peptide: Gag polyprotein
Keywordscapsid / Gag / foamy virus / pentamer / VIRAL PROTEIN
Function / homology
Function and homology information


host cytoskeleton / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / host cell / viral nucleocapsid / host cell cytoplasm / symbiont entry into host cell / host cell nucleus
Similarity search - Function
Gag polyprotein / : / Spumavirus gag protein, N-terminal / Spumavirus Gag polyprotein, conserved central domain / Spumavirus Gag polyprotein, C-terminal
Similarity search - Domain/homology
Biological speciesEastern chimpanzee simian foamy virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
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_17313.png

Downloads & links

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Map

FileDownload / File: emd_17313.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0137
Minimum - Maximum-0.056472808 - 0.08967932
Average (Standard dev.)0.00023862175 (±0.002804748)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17313_msk_1.map
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Half map: #1

Fileemd_17313_half_map_1.map
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Half map: #2

Fileemd_17313_half_map_2.map
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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
    • Protein or peptide: Gag polyprotein

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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: all / NCBI-ID: 2170195 / Sci species name: Eastern chimpanzee simian foamy virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Macromolecule #1: Gag polyprotein

MacromoleculeName: Gag polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Eastern chimpanzee simian foamy virus
Molecular weightTheoretical: 70.693414 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASGSNVEEY ELDVEALVVI LRDRNIPRNP LHGEVIGLRL TEGWWGQIER FQMVRLILQN DDNEPLQRPR YEVIQRAVNP HTMFMISGP LAELQLAFQD LDLPEGPLRF GPLANGHYVQ GDPYSSSYRP VTMAETAQMT RDELEDVLNT QSEIEIQMIN L LELYEVET ...String:
MASGSNVEEY ELDVEALVVI LRDRNIPRNP LHGEVIGLRL TEGWWGQIER FQMVRLILQN DDNEPLQRPR YEVIQRAVNP HTMFMISGP LAELQLAFQD LDLPEGPLRF GPLANGHYVQ GDPYSSSYRP VTMAETAQMT RDELEDVLNT QSEIEIQMIN L LELYEVET RALRRQLAER SSTGQGGISP GAPRSRPPVS SFSGLPSLPS IPGIHPRAPS PPRATSTPGN IPWSLGDDNP PS SSFPGPS QPRVSFHPGN PFVEEEGHRP RSQSRERRRE ILPAPVPSAP PMIQYIPVPP PPPIGTVIPI QHIRSVTGEP PRN PREIPI WLGRNAPAID GVFPVTTPDL RCRIINAILG GNIGLSLTPG DCLTWDSAVA TLFIRTHGTF PMHQLGNVIK GIVD QEGVA TAYTLGMMLS GQNYQLVSGI IRGYLPGQAV VTALQQRLDQ EIDDQTRAET FIQHLNAVYE ILGLNARGQS IRASV TPQP RPSRGRGRGQ NTSRPSQGPA NSGRGRQRPA SGQSNRGSST QNQNQDNLNQ GGYNLRPRTY QPQRYGGGRG RRWNDN TNN QESRPSDQGS QTPRPNQAGS GVRGNQSQTP RPAAGRGGRG NHNRNQRSSG AGDSRAVNTV TQSATSSTDE SSSAVTA AS GGDQRD

UniProtKB: Gag polyprotein

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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: 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK III

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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) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Average electron dose: 48.0 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: 4.0 µm / Nominal defocus min: 1.0 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

Particle selectionNumber selected: 52141
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 97872
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT
Output model

PDB-8ozl:
In situ cryoEM structure of the Prototype Foamy Virus capsid, pentamer localised reconstruction

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