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- PDB-8wcm: NSs filament formation determines RVFV pathogenesis -

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Basic information

Entry
Database: PDB / ID: 8wcm
TitleNSs filament formation determines RVFV pathogenesis
ComponentsNon-structural protein NS-S
KeywordsVIRAL PROTEIN / Self-assembly / helical structure
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
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsLi, H. / Rao, G. / Cao, S. / Peng, K.
Funding support China, 1items
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, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / em_admin / em_author_list / pdbx_entry_details
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _em_admin.last_update / _em_author_list.author
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.3Dec 11, 2024Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-structural protein NS-S
B: Non-structural protein NS-S


Theoretical massNumber of molelcules
Total (without water)61,7402
Polymers61,7402
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "B"
d_2ens_1chain "A"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 2 - 244 / Label seq-ID: 11 - 253

Dom-IDAuth asym-IDLabel asym-ID
d_1BB
d_2AA

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Components

#1: Protein Non-structural protein NS-S


Mass: 30870.221 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rift Valley fever virus / Gene: NSs / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A2SZZ6
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: The self-assembly of RVFV NSs protein / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Rift Valley fever virus
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.18.2_3874: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 83.437 ° / Axial rise/subunit: 14.584 Å / Axial symmetry: C1
3D reconstructionResolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 617585 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 53.53 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00793942
ELECTRON MICROSCOPYf_angle_d0.70325358
ELECTRON MICROSCOPYf_chiral_restr0.0489596
ELECTRON MICROSCOPYf_plane_restr0.0045702
ELECTRON MICROSCOPYf_dihedral_angle_d11.9837536
Refine LS restraints NCSType: NCS constraints / Rms dev position: 0.000702714676888 Å

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