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- PDB-9umz: Cryo-EM structure of the SFTSV NP-RNA complex -

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Basic information

Entry
Database: PDB / ID: 9umz
TitleCryo-EM structure of the SFTSV NP-RNA complex
Components
  • Nucleoprotein
  • RNA (28-MER)
KeywordsNUCLEAR PROTEIN/RNA / SFTSV / N protein / RNP complex / NUCLEAR PROTEIN-RNA complex
Function / homology
Function and homology information


viral nucleocapsid / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / ribonucleoprotein complex / host cell nucleus / RNA binding
Similarity search - Function
Nucleocapsid, Phlebovirus/Tenuivirus / Nucleocapsid, Phlebovirus / Tenuivirus/Phlebovirus nucleocapsid protein
Similarity search - Domain/homology
RNA / RNA (> 10) / Nucleoprotein
Similarity search - Component
Biological speciesSFTS virus HB29
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.98 Å
AuthorsWang, Y. / Wu, H. / Deng, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: mBio / Year: 2025
Title: Structural insight into RNA encapsidation by the severe fever with thrombocytopenia syndrome virus nucleocapsid protein.
Authors: Yong Wang / Hao Wu / Jiawen Sun / Wenhua Kuang / Hualin Wang / Yun-Jia Ning / Zengqin Deng /
Abstract: Severe fever with thrombocytopenia syndrome virus (SFTSV), an emerging highly pathogenic bunyavirus, poses a significant public health threat with a case fatality rate of up to 30%. The viral ...Severe fever with thrombocytopenia syndrome virus (SFTSV), an emerging highly pathogenic bunyavirus, poses a significant public health threat with a case fatality rate of up to 30%. The viral nucleocapsid protein (NP) encapsidates the genomic RNA to form a ribonucleoprotein (RNP) complex, which is critical for transcription and replication. However, the molecular mechanism underlying SFTSV RNA encapsidation remains poorly understood, largely due to the lack of structural information on the NP-RNA complex. Here, we report a cryo-electron microscopy structure of the SFTSV NP in complex with single-stranded RNA. The structure reveals a pentameric NP assembly that sequesters RNA along the inner surface of the oligomeric ring in a sequence-independent manner. Strikingly, all the RNA bases face the protein, rendering them inaccessible for transcription and replication. Each NP subunit accommodates four nucleotides within an evolutionarily conserved hydrophobic cleft, with an additional two to three nucleotides bound at the inter-subunit interface. The functional importance of the NP-RNA interactions is further corroborated by a minigenome-based assay. This work provides structural insight into RNA encapsidation by SFTSV NP and offers a foundation for the rational design of antiviral therapeutics targeting this essential viral protein.IMPORTANCESevere fever with thrombocytopenia syndrome virus (SFTSV) is a highly pathogenic bunyavirus that causes severe hemorrhagic fever, leukopenia, thrombocytopenia, and multi-organ failure, with a case fatality rate of up to 30%. No licensed vaccines or specific antiviral therapies are currently available. The viral nucleocapsid protein (NP) is essential for viral transcription and replication, forming a ribonucleoprotein complex (RNP) by encapsidating viral genomic RNA. However, the structural basis of RNA recognition and encapsidation by SFTSV NP remains poorly understood. In this study, we determined a cryo-electron microscopy structure of the SFTSV NP-RNA complex. Structural comparisons and evolutionary conservation analysis of NPs across the family Phenuiviridae uncovered a conserved RNA-binding mode among phenuiviruses, suggesting a shared RNA encapsidation mechanism among related viruses. Our findings provide critical structural insights into SFTSV RNA encapsidation and will aid future efforts to develop antivirals against SFTSV and related pathogenic viruses.
History
DepositionApr 23, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein
D: Nucleoprotein
E: Nucleoprotein
K: RNA (28-MER)


Theoretical massNumber of molelcules
Total (without water)143,6146
Polymers143,6146
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 27017.234 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SFTS virus HB29 / Gene: NP / Production host: Escherichia coli (E. coli) / References: UniProt: P0DW82
#2: RNA chain RNA (28-MER)


Mass: 8527.686 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: SFTSV NP-RNA / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: SFTS virus HB29
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
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 software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13Coot3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 63930 / Symmetry type: POINT
RefinementHighest resolution: 3.98 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00210261
ELECTRON MICROSCOPYf_angle_d0.55314007
ELECTRON MICROSCOPYf_dihedral_angle_d8.3811647
ELECTRON MICROSCOPYf_chiral_restr0.0381624
ELECTRON MICROSCOPYf_plane_restr0.0041686

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