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- EMDB-19347: Cryo-EM structure of a Foamy Virus fusion glycoprotein stabilized... -

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Basic information

Entry
Database: EMDB / ID: EMD-19347
TitleCryo-EM structure of a Foamy Virus fusion glycoprotein stabilized in the prefusion conformation
Map dataSharpened map of a stabilized Foamy Virus envelope glycoprotein ectodomain
Sample
  • Complex: Gorilla Foamy Virus Envelope glycoprotein
    • Protein or peptide: Envelope glycoprotein gp130
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsEnvelope / Fusion / Spumavirus / VIRUS
Function / homologyFoamy virus envelope protein / Foamy virus envelope protein / host cell endoplasmic reticulum membrane / viral envelope / virion membrane / membrane / Envelope glycoprotein gp130
Function and homology information
Biological speciesSpumavirus / Simian foamy virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsFernandez I / Backovic M
Funding support France, 1 items
OrganizationGrant numberCountry
Laboratories of Excellence (LabEx)ANR-LBX-62 IBEID France
CitationJournal: Sci Adv / Year: 2024
Title: Structures of the Foamy virus fusion protein reveal an unexpected link with the F protein of paramyxo- and pneumoviruses.
Authors: Ignacio Fernández / François Bontems / Delphine Brun / Youna Coquin / Casper A Goverde / Bruno E Correia / Antoine Gessain / Florence Buseyne / Felix A Rey / Marija Backovic /
Abstract: Foamy viruses (FVs) constitute a subfamily of retroviruses. Their envelope (Env) glycoprotein drives the merger of viral and cellular membranes during entry into cells. The only available structures ...Foamy viruses (FVs) constitute a subfamily of retroviruses. Their envelope (Env) glycoprotein drives the merger of viral and cellular membranes during entry into cells. The only available structures of retroviral Envs are those from human and simian immunodeficiency viruses from the subfamily of orthoretroviruses, which are only distantly related to the FVs. We report the cryo-electron microscopy structures of the FV Env ectodomain in the pre- and post-fusion states, which unexpectedly demonstrate structural similarity with the fusion protein (F) of paramyxo- and pneumoviruses, implying an evolutionary link between the viral fusogens. We describe the structural features that are unique to the FV Env and propose a mechanistic model for its conformational change, highlighting how the interplay of its structural elements could drive membrane fusion and viral entry. The structural knowledge on the FV Env now provides a framework for functional investigations, which can benefit the design of FV Env variants with improved features for use as gene therapy vectors.
History
DepositionJan 4, 2024-
Header (metadata) releaseOct 23, 2024-
Map releaseOct 23, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19347.png

Downloads & links

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Map

FileDownload / File: emd_19347.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of a stabilized Foamy Virus envelope glycoprotein ectodomain
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 320 pix.
= 304. Å		0.95 Å/pix.
x 320 pix.
= 304. Å		0.95 Å/pix.
x 320 pix.
= 304. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0152
Minimum - Maximum-0.003213411 - 1.984
Average (Standard dev.)0.0018971637 (±0.031766556)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 304.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19347_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map

Fileemd_19347_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_19347_half_map_1.map
AnnotationHalf_map_A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_19347_half_map_2.map
AnnotationHalf_map_B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Gorilla Foamy Virus Envelope glycoprotein

EntireName: Gorilla Foamy Virus Envelope glycoprotein
Components
  • Complex: Gorilla Foamy Virus Envelope glycoprotein
    • Protein or peptide: Envelope glycoprotein gp130
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Gorilla Foamy Virus Envelope glycoprotein

SupramoleculeName: Gorilla Foamy Virus Envelope glycoprotein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Spumavirus

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Macromolecule #1: Envelope glycoprotein gp130

MacromoleculeName: Envelope glycoprotein gp130 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Simian foamy virus
Molecular weightTheoretical: 101.784508 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: SRIQWNKDIQ VLGPVIDWNV TQRAVYQPLQ LRRIAAALRA QHPVPKYVEV NMTSIPQGVF YQPHPEPIIH TERVLGLSQV LMINSENVA NSANLSQETK ALLTEMVNEE MQGLSDVMID FEIPLGDPRD QEQYIHRKCY QEFAHCYLVK YKTPQPWPNE G LIADQCPL ...String:
SRIQWNKDIQ VLGPVIDWNV TQRAVYQPLQ LRRIAAALRA QHPVPKYVEV NMTSIPQGVF YQPHPEPIIH TERVLGLSQV LMINSENVA NSANLSQETK ALLTEMVNEE MQGLSDVMID FEIPLGDPRD QEQYIHRKCY QEFAHCYLVK YKTPQPWPNE G LIADQCPL PGLADVSFYP YQAIWDYYAK IENIRPANWT SSKLYGKARM GSYYIPKRLR NINNTHILFC SDVLYSKWYN LQ NSILQNE NELTKRLSNL TIGNKLKNRA LPYEWAKGGL NRLFRNISVL DVCSRPEMVL LLNKTYYTFS LWEGDCNITR YNV NETVPE CKDFPHRRFN DHPYSCRLWR YREGKEEVKC LTSDHTRCLY YPEYSNPEAL FDFGFLSYMR NFPGPQCIES TSIR QQDYE VYSIYQECKL ASKTYGIDSV LFSLKNFLNY TGKPVNEMPN ARAFVGLIDP KFPPTYPNIT RDQYQGCNIN QGGGG SGGG GSEVNNNYSK LRSMGYALTG AVQTLAQISD INDQNLQQGI YLLRDHIVTL MEATLHDISI MPGMFAVQHV HTHLNH LRT MLMERRIDWT YMSSSWLQTQ LQKSDDEMKV IKRTARSLVY YVKQTYNSLT ATAWEIGLYY ELIIPRHIYL NNWQIVN IG HLIKSAGQLT HVTLSHPYEI INRECSNTLY LHLEECRRLD YVICDVVKIV QPCGNSSDSS DCPVWAEPVK EPHVQISP L KNGSYLVLAS STDCQIPPYV PSVVTVNETT QCFGVTFKKP LVAEEKTSLE PQLPHLQLRL PHLVGIIAKI KGIKIEVTS SGESIKDQLE RAKAELLRLD IHESAIGGYI PEAPRDGQAY VRKDGEWVLL STFLGDDDDK AGWSHPQFEK GGGSGGGSGG GSWSHPQFE K

UniProtKB: Envelope glycoprotein gp130, Envelope glycoprotein gp130

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 15 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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: 8
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Details: Performed twice
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm

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Image processing

Startup modelType of model: NONE / Details: ab-initio generated model
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15471
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 5 / Software - Name: cryoSPARC

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-8rm0:
Cryo-EM structure of a Foamy Virus fusion glycoprotein stabilized in the prefusion conformation

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