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- EMDB-50530: Cryo-EM map of a Gorilla Foamy Virus fusion glycoprotein stabiliz... -

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Basic information

Entry
Database: EMDB / ID: EMD-50530
TitleCryo-EM map of a Gorilla Foamy Virus fusion glycoprotein stabilized in the prefusion conformation (C1 symmetry)
Map dataSharpened map, C1 symmetry
Sample
  • Complex: Gorilla Foamy Virus Envelope glycoprotein
    • Other: Foamy Virus Env
KeywordsEnvelope / Fusion / Spumavirus / VIRUS
Biological speciesSpumavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 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
DepositionJun 4, 2024-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50530.png

Downloads & links

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Map

FileDownload / File: emd_50530.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map, C1 symmetry
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: 0.0456
Minimum - Maximum-0.003594643 - 2.020659
Average (Standard dev.)0.0017932383 (±0.0295536)
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_50530_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Refined map, C1 symmetry

Fileemd_50530_additional_1.map
AnnotationRefined map, C1 symmetry
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_50530_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_50530_half_map_2.map
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
    • Other: Foamy Virus Env

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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: all
Source (natural)Organism: Spumavirus

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Macromolecule #1: Foamy Virus Env

MacromoleculeName: Foamy Virus Env / type: other / ID: 1 / Classification: other
Source (natural)Organism: Spumavirus
SequenceString: RSSRIQWNKD IQVLGPVIDW NVTQRAVYQP LQLRRIAAAL RAQHPVPKYV EVNMTSIPQG VFYQPHPEPI IHTERVLGLS QVLMINSENV ANSANLSQET KALLTEMVNE EMQGLSDVMI DFEIPLGDPR DQEQYIHRKC YQEFAHCYLV KYKTPQPWPN EGLIADQCPL ...String:
RSSRIQWNKD IQVLGPVIDW NVTQRAVYQP LQLRRIAAAL RAQHPVPKYV EVNMTSIPQG VFYQPHPEPI IHTERVLGLS QVLMINSENV ANSANLSQET KALLTEMVNE EMQGLSDVMI DFEIPLGDPR DQEQYIHRKC YQEFAHCYLV KYKTPQPWPN EGLIADQCPL PGLADVSFYP YQAIWDYYAK IENIRPANWT SSKLYGKARM GSYYIPKRLR NINNTHILFC SDVLYSKWYN LQNSILQNEN ELTKRLSNLT IGNKLKNRAL PYEWAKGGLN RLFRNISVLD VCSRPEMVLL LNKTYYTFSL WEGDCNITRY NVNETVPECK DFPHRRFNDH PYSCRLWRYR EGKEEVKCLT SDHTRCLYYP EYSNPEALFD FGFLSYMRNF PGPQCIESTS IRQQDYEVYS IYQECKLASK TYGIDSVLFS LKNFLNYTGK PVNEMPNARA FVGLIDPKFP PTYPNITRDQ YQGCNINQGG GGSGGGGSEV NNNYSKLRSM GYALTGAVQT LAQISDINDQ NLQQGIYLLR DHIVTLMEAT LHDISIMPGM FAVQHVHTHL NHLRTMLMER RIDWTYMSSS WLQTQLQKSD DEMKVIKRTA RSLVYYVKQT YNSLTATAWE IGLYYELIIP RHIYLNNWQI VNIGHLIKSA GQLTHVTLSH PYEIINRECS NTLYLHLEEC RRLDYVICDV VKIVQPCGNS SDSSDCPVWA EPVKEPHVQI SPLKNGSYLV LASSTDCQIP PYVPSVVTVN ETTQCFGVTF KKPLVAEEKT SLEPQLPHLQ LRLPHLVGII AKIKGIKIEV TSSGESIKDQ LERAKAELLR LDIHESAIGG YIPEAPRDGQ AYVRKDGEWV LLSTFLGDDD DKAGWSHPQF EKGGGSGGGS GGGSWSHPQF EK

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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 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
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: 4.2 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

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