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

Validation slider image for 9VDZ

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 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.

Macromolecule Content 

  • Total Structure Weight: 173.62 kDa 
  • Atom Count: 11,704 
  • Modeled Residue Count: 1,486 
  • Deposited Residue Count: 1,576 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
hA5-6(W30B/E45) Fab heavy chainA,
E [auth H]
232Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
hA5-6(W30B/E45) Fab light chainB,
F [auth L]
218Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
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 GlycosylationD 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