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- EMDB-19348: Cryo-EM structure of a Foamy Virus fusion glycoprotein in the pos... -

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Basic information

Entry
Database: EMDB / ID: EMD-19348
TitleCryo-EM structure of a Foamy Virus fusion glycoprotein in the postfusion conformation
Map data
Sample
  • Complex: Gorilla Foamy Virus Envelope glycoprotein
    • Protein or peptide: Envelope glycoprotein gp130
  • 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: 3.1 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-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19348.png

Downloads & links

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Map

FileDownload / File: emd_19348.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 352 pix.
= 302.72 Å		0.86 Å/pix.
x 352 pix.
= 302.72 Å		0.86 Å/pix.
x 352 pix.
= 302.72 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00603
Minimum - Maximum-0.057551213 - 0.101282805
Average (Standard dev.)0.000046144127 (±0.0025398359)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 302.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_19348_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_19348_half_map_2.map
Projections & Slices
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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
  • 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: 52.050996 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: ALRAQHPVPK YVEVNMTSIP QGVFYQPHPE PIIHTERVLG LSQVLMINSE NVANSANLSQ ETKALLTEMV NEEMQGLSDV MIDFEIPLG DPRDQEQYIH RKCYQEFAHC YLVKYKTPQP WPNEGLIADQ CPLPGLADVS FYPYQAIWDY YAKIENIRPA N WTSSKLYG ...String:
ALRAQHPVPK YVEVNMTSIP QGVFYQPHPE PIIHTERVLG LSQVLMINSE NVANSANLSQ ETKALLTEMV NEEMQGLSDV MIDFEIPLG DPRDQEQYIH RKCYQEFAHC YLVKYKTPQP WPNEGLIADQ CPLPGLADVS FYPYQAIWDY YAKIENIRPA N WTSSKLYG KARMGSYYIP KRLRNINNTH ILFCSDVLYS KWYNLQNSIL QNENELTKRL SNLTIGNKLK NRALPYEWAK GG LNRLFRN ISVLDVCSRP EMVLLLNKTY YTFSLWEGDC NITRYNVNET VPECKDFPHR RFNDHPYSCR LWRYREGKEE VKC LTSDHT RCLYYPEYSN PEALFDFGFL SYMRNFPGPQ CIESTSIRQQ DYEVYSIYQE CKLASKTYGI DSVLFSLKNF LNYT GKPVN EMPNARAFVG LIDPKFPPTY PNITRDQYQG CNINQRRKR

UniProtKB: Envelope glycoprotein gp130

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Macromolecule #2: Envelope glycoprotein gp130

MacromoleculeName: Envelope glycoprotein gp130 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Simian foamy virus
Molecular weightTheoretical: 42.067801 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: EVNNNYSKLR SMGYALTGAV QTLAQISDIN DQNLQQGIYL LRDHIVTLME ATLHDISIME GMFAVQHVHT HLNHLRTMLM ERRIDWTYM SSSWLQTQLQ KSDDEMKVIK RTARSLVYYV KQTYNSLTAT AWEIGLYYEL IIPRHIYLNN WQIVNIGHLI K SAGQLTHV ...String:
EVNNNYSKLR SMGYALTGAV QTLAQISDIN DQNLQQGIYL LRDHIVTLME ATLHDISIME GMFAVQHVHT HLNHLRTMLM ERRIDWTYM SSSWLQTQLQ KSDDEMKVIK RTARSLVYYV KQTYNSLTAT AWEIGLYYEL IIPRHIYLNN WQIVNIGHLI K SAGQLTHV TLSHPYEIIN RECSNTLYLH LEECRRLDYV ICDVVKIVQP CGNSSDSSDC PVWAEPVKEP HVQISPLKNG SY LVLASST DCQIPPYVPS VVTVNETTQC FGVTFKKPLV AEEKTSLEPQ LPHLQLRLPH LVGIIAKIKG IKIEVTSSGE SIK DQLERA KAELLRLDIH EDDDDKAGWS HPQFEKGGGS GGGSGGGSWS HPQFEK

UniProtKB: Envelope glycoprotein gp130

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 3 / 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 R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 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: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE / Details: ab-initio generated model
Final reconstructionNumber classes used: 2 / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 98407
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 4 / Software - Name: RELION

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Atomic model buiding 1

Initial model
ChainDetailsPDB ID
source_name: Other, initial_model_type: otherPhenix map to model tool followed by manual building
source_name: PDB, initial_model_type: experimental model

8aez

Output model

PDB-8rm1:
Cryo-EM structure of a Foamy Virus fusion glycoprotein in the postfusion conformation

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