8XK8 | pdb_00008xk8

N1D10 Fab bound to SFTSV glycoprotein-Gn


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.53 Å
  • R-Value Free: 
    0.324 (Depositor), 0.324 (DCC) 
  • R-Value Work: 
    0.250 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 
    0.254 (Depositor) 

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

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This is version 1.3 of the entry. See complete history

Literature

A broadly protective antibody targeting glycoprotein Gn inhibits severe fever with thrombocytopenia syndrome virus infection.

Ren, X.Sun, J.Kuang, W.Yu, F.Wang, B.Wang, Y.Deng, W.Xu, Z.Yang, S.Wang, H.Hu, Y.Deng, Z.Ning, Y.J.Zhao, H.

(2024) Nat Commun 15: 7009-7009

  • DOI: https://doi.org/10.1038/s41467-024-51108-z

  • PubMed Abstract: 

    Severe fever with thrombocytopenia syndrome virus (SFTSV) is an emerging bunyavirus that causes severe viral hemorrhagic fever and thrombocytopenia syndrome with a fatality rate of up to 30%. No licensed vaccines or therapeutics are currently available for humans. Here, we develop seven monoclonal antibodies (mAbs) against SFTSV surface glycoprotein Gn. Mechanistic studies show that three neutralizing mAbs (S2A5, S1G3, and S1H7) block multiple steps during SFTSV infection, including viral attachment and membrane fusion, whereas another neutralizing mAb (B1G11) primarily inhibits the viral attachment step. Epitope binning and X-ray crystallographic analyses reveal four distinct antigenic sites on Gn, three of which have not previously been reported, corresponding to domain I, domain II, and spanning domain I and domain II. One of the most potent neutralizing mAbs, S2A5, binds to a conserved epitope on Gn domain I and broadly neutralizes infection of six SFTSV strains corresponding to genotypes A to F. A single dose treatment of S2A5 affords both pre- and post-exposure protection of mice against lethal SFTSV challenge without apparent weight loss. Our results support the importance of glycoprotein Gn for eliciting a robust humoral response and pave a path for developing prophylactic and therapeutic antibodies against SFTSV infection.


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

Macromolecule Content 

  • Total Structure Weight: 183.83 kDa 
  • Atom Count: 11,394 
  • Modeled Residue Count: 1,496 
  • Deposited Residue Count: 1,684 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelopment polyprotein
A, B
357Severe fever with thrombocytopenia syndrome virusMutation(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
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
mAb N1D10 Fab heavy chainC [auth H],
E [auth C]
247Mus musculusMutation(s): 0 
Gene Names: Fab heavy chain
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
mAb N1D10 Fab light chainD [auth L],
F [auth D]
238Mus musculusMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.53 Å
  • R-Value Free:  0.324 (Depositor), 0.324 (DCC) 
  • R-Value Work:  0.250 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 0.254 (Depositor) 
Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.124α = 90
b = 111.909β = 94.33
c = 87.856γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata scaling
DIALSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-10
    Type: Initial release
  • Version 1.1: 2024-07-24
    Changes: Database references
  • Version 1.2: 2024-09-11
    Changes: Database references
  • Version 1.3: 2024-11-06
    Changes: Structure summary