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- EMDB-37443: NSs filament formation determines RVFV pathogenesis -

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Basic information

Entry
Database: EMDB / ID: EMD-37443
TitleNSs filament formation determines RVFV pathogenesis
Map dataEM map
Sample
  • Complex: The self-assembly of RVFV NSs protein
    • Protein or peptide: Non-structural protein NS-S
KeywordsSelf-assembly / helical structure / VIRAL PROTEIN
Function / homologyPhlebovirus, non structural protein / Rift valley fever virus non structural protein-like / Rift valley fever virus non structural protein (NSs) like / Non-structural protein NS-S
Function and homology information
Biological speciesRift Valley fever virus
Methodhelical reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsLi H / Rao G / Cao S / Peng K
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC2303300 China
CitationJournal: Cell / Year: 2024
Title: Rift Valley fever virus coordinates the assembly of a programmable E3 ligase to promote viral replication.
Authors: Huiling Li / Yulan Zhang / Guibo Rao / Chongtao Zhang / Zhenqiong Guan / Ziyan Huang / Shufen Li / Pierre-Yves Lozach / Sheng Cao / Ke Peng /
Abstract: Viruses encode strategies to degrade cellular proteins to promote infection and pathogenesis. Here, we revealed that the non-structural protein NSs of Rift Valley fever virus forms a filamentous E3 ...Viruses encode strategies to degrade cellular proteins to promote infection and pathogenesis. Here, we revealed that the non-structural protein NSs of Rift Valley fever virus forms a filamentous E3 ligase to trigger efficient degradation of targeted proteins. Reconstitution in vitro and cryoelectron microscopy analysis with the 2.9-Å resolution revealed that NSs forms right-handed helical fibrils. The NSs filamentous oligomers associate with the cellular FBXO3 to form a remodeled E3 ligase. The NSs-FBXO3 E3 ligase targets the cellular TFIIH complex through the NSs-P62 interaction, leading to ubiquitination and proteasome-dependent degradation of the TFIIH complex. NSs-FBXO3-triggered TFIIH complex degradation resulted in robust inhibition of antiviral immunity and promoted viral pathogenesis in vivo. Furthermore, it is demonstrated that NSs can be programmed to target additional proteins for proteasome-dependent degradation, serving as a versatile targeted protein degrader. These results showed that a virulence factor forms a filamentous and programmable degradation machinery to induce organized degradation of cellular proteins to promote viral infection.
History
DepositionSep 13, 2023-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateDec 11, 2024-
Current statusDec 11, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37443.png

Downloads & links

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Map

FileDownload / File: emd_37443.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 256 pix.
= 243.2 Å		0.95 Å/pix.
x 256 pix.
= 243.2 Å		0.95 Å/pix.
x 256 pix.
= 243.2 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: 0.17
Minimum - Maximum-0.81646717 - 1.4058331
Average (Standard dev.)0.005984196 (±0.0687474)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 243.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: EM half map

Fileemd_37443_half_map_1.map
AnnotationEM half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EM half map

Fileemd_37443_half_map_2.map
AnnotationEM half 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 : The self-assembly of RVFV NSs protein

EntireName: The self-assembly of RVFV NSs protein
Components
  • Complex: The self-assembly of RVFV NSs protein
    • Protein or peptide: Non-structural protein NS-S

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Supramolecule #1: The self-assembly of RVFV NSs protein

SupramoleculeName: The self-assembly of RVFV NSs protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rift Valley fever virus

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Macromolecule #1: Non-structural protein NS-S

MacromoleculeName: Non-structural protein NS-S / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rift Valley fever virus
Molecular weightTheoretical: 30.870221 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: HHHHHHGSGG DYFPVISVDL QSGRRVVSVE YIRGDGPPRI PYSMVGPCCV FLMHHRPSHE VRLRFSDFYN VGEFPYRVGL GDFASNVAP PPAKPFQRLI DLIGHMTLSD FTRFPNLKEA ISWPLGEPSL AFFDLSSTRV HRNDDIRRDQ IATLAMRSCK I TNDLEDSF ...String:
HHHHHHGSGG DYFPVISVDL QSGRRVVSVE YIRGDGPPRI PYSMVGPCCV FLMHHRPSHE VRLRFSDFYN VGEFPYRVGL GDFASNVAP PPAKPFQRLI DLIGHMTLSD FTRFPNLKEA ISWPLGEPSL AFFDLSSTRV HRNDDIRRDQ IATLAMRSCK I TNDLEDSF VGLHRMIVTE AILRGIDLCL LPGFDLMYEV AHVQCVRLLQ AAKEDISNAV VPNSALIALM EESLMLRSSL PS MMGRNNW IPVVPPIPDV EMESEEESDD DGFVEVD

UniProtKB: Non-structural protein NS-S

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 14.584 Å
Applied symmetry - Helical parameters - Δ&Phi: 83.437 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 617585
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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