8XK5 | pdb_00008xk5

SNB1G11 Fab bound to SFTSV glycoprotein Gn


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 
    0.281 (Depositor), 0.283 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8XK5

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
  • Primary Citation Related Structures: 
    8XK5, 8XK6, 8XK8

  • 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: 464.52 kDa 
  • Atom Count: 27,019 
  • Modeled Residue Count: 3,499 
  • Deposited Residue Count: 4,230 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
mAb SNB1G11 Fab heavy chainA,
D [auth C],
G [auth I],
J [auth N],
M [auth G]
256Mus musculusMutation(s): 0 
Gene Names: Fab heavy chain
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
mAb SNB1G11 Fab light chainB,
E [auth D],
H [auth J],
K [auth O],
N [auth H]
233Mus musculusMutation(s): 0 
Gene Names: Fab light chain
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelopment polyproteinC [auth E],
F,
I [auth K],
L [auth R],
O [auth L]
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
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free:  0.281 (Depositor), 0.283 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.67α = 90
b = 180.96β = 90
c = 263.95γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
xia2data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data

  • Released Date: 2024-07-10 
  • Deposition Author(s): Deng, Z.

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: 2024-11-13
    Changes: Structure summary