9VDZ | pdb_00009vdz

hA5-6(W30B/E45) Fab bound to SFTSV glycoprotein Gn


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 
    0.256 (Depositor), 0.256 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Humanization and engineering of protective antibodies targeting severe fever with thrombocytopenia syndrome virus Gn protein.

Ren, X.Deng, W.Yu, F.Kuang, W.Na, H.Yang, S.Sun, J.Xu, J.Shu, B.Cao, S.Ke, X.Deng, Z.Ning, Y.J.Zhao, H.

(2026) Cell Rep 45: 116936-116936

  • DOI: https://doi.org/10.1016/j.celrep.2026.116936
  • Primary Citation of Related Structures:  
    9VDY, 9VDZ, 9VE0

  • PubMed Abstract: 

    Severe fever with thrombocytopenia syndrome virus (SFTSV) is a highly lethal tick-borne bunyavirus with no approved therapies. We previously developed a murine-human chimeric antibody S2A5, which provides complete protection against lethal SFTSV infection, but its clinical use is limited by potential immunogenicity and moderate activity against certain genotypes. Here, we systematically humanize and optimize S2A5 using five complementary computational platforms, generating eleven variants and identifying hA5-6, which retains potent neutralizing activity and confers full protection in mice. Structure-guided engineering and in silico mutational analysis further improve antibody function, yielding two optimized hA5-6 variants with up to a 317-fold increase in neutralization potency. Biochemical and functional assays, together with cryo-EM reconstruction of an optimized variant bound to SFTSV virions, indicate that the enhanced activity is associated with improved binding to recombinant Gn and intact virions. This study identifies promising SFTSV therapeutics and establishes a generalizable antibody optimization framework.


  • Organizational Affiliation
    • State Key Laboratory of Virology and Biosafety, College of Life Sciences, Wuhan University, Wuhan, Hubei, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
hA5-6(W30B/E45) Fab heavy chainA,
E [auth H]
232Homo sapiensMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
hA5-6(W30B/E45) Fab light chainB,
F [auth L]
218Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Envelopment polyprotein
C, D
338Severe fever with thrombocytopenia syndrome virusMutation(s): 0 
UniProt
Find proteins for W5VWE0 (Dabie bandavirus)
Explore W5VWE0 
Go to UniProtKB:  W5VWE0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW5VWE0
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG,
H [auth J]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G62182OO
GlyCosmos:  G62182OO
GlyGen:  G62182OO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free:  0.256 (Depositor), 0.256 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.2α = 90
b = 91.36β = 90
c = 309.8γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-07
    Type: Initial release
  • Version 1.1: 2026-02-25
    Changes: Database references