9UB6 | pdb_00009ub6

Crystal structure of SFTSV Gn head with nanobody Nb261


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 
    0.221 (Depositor) 
  • R-Value Work: 
    0.191 (Depositor) 
  • R-Value Observed: 
    0.193 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9UB6

This is version 1.1 of the entry. See complete history

Literature

A rationally designed cocktail of nanobodies elicited by heterologous vaccination confers protection against SFTSV in preclinical models.

Wu, X.Zhu, L.Liang, S.Chang, Z.Wang, Y.Zou, Q.Xu, Z.Zhang, D.Hu, J.Geng, S.Li, Z.Yu, W.Hu, Z.Chen, M.Cao, K.Jia, B.Wei, H.Cai, R.Long, J.Yang, X.Yang, Q.Yu, Z.Shi, L.Xu, B.Zheng, Y.Meng, S.Cai, J.Zhou, G.Zhu, K.Dou, Y.Lou, Z.Li, M.Wu, Y.Wu, Z.

(2025) Sci Transl Med 17: eady9025-eady9025

  • DOI: https://doi.org/10.1126/scitranslmed.ady9025
  • Primary Citation Related Structures: 
    9UB6

  • PubMed Abstract: 

    Severe fever with thrombocytopenia syndrome virus (SFTSV), an emerging tick-borne phlebovirus, poses a growing public health threat, with no approved vaccines or targeted therapies. Its genetic diversity and rapid reassortment have hindered the development of broadly effective interventions. Here, we isolated and characterized broadly neutralizing camelid nanobodies generated by a heterologous immunization strategy. These nanobodies exhibited cross-subtype neutralization and conferred protection against disease in humanized and lethal murine models of SFTSV infection. Structural analysis revealed binding to distinct, nonoverlapping epitopes on the viral glycoprotein complex. A rationally designed cocktail leveraging this epitope diversity achieved complete viral inhibition through synergistic mechanisms. In both murine and immunocompetent ferret models, the cocktail enabled efficient viral clearance and full protection against lethal challenge. These results demonstrate the therapeutic potential of nanobody cocktails for SFTSV infection and establish a generalizable framework for nanobody-based countermeasures against genetically variable emerging viruses, including other members of the Bunyavirales order.


  • Organizational Affiliation
    • Center for Public Health Research, Medical School, Nanjing University, Nanjing 210093, China.

Macromolecule Content 

  • Total Structure Weight: 48.81 kDa 
  • Atom Count: 3,350 
  • Modeled Residue Count: 425 
  • Deposited Residue Count: 433 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycoprotein N318SFTS virus HB29Mutation(s): 0 
UniProt
Find proteins for R4V2Q5 (Dabie bandavirus)
Explore R4V2Q5 
Go to UniProtKB:  R4V2Q5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupR4V2Q5
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Nanobody VHH261115Homo sapiensMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO
GlyCosmos: G22768VO
GlyGen: G22768VO

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
D [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free:  0.221 (Depositor) 
  • R-Value Work:  0.191 (Depositor) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 172.71α = 90
b = 172.71β = 90
c = 136.03γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32090014

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-22
    Type: Initial release
  • Version 1.1: 2026-05-06
    Changes: Database references, Structure summary