9LU3 | pdb_00009lu3

LN1F9 Fab bound to Nipah Virus attachment (G) glycoprotein head domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.269 (Depositor), 0.268 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Antigenic landscape of Nipah virus attachment glycoprotein analysis reveals a protective immunodominant epitope across species.

Zhou, D.Wang, Y.Yao, Y.Kuang, W.Cheng, R.Zhang, G.Liu, H.Li, X.Chiu, S.Deng, Z.Zhao, H.

(2025) NPJ Vaccines 

  • DOI: https://doi.org/10.1038/s41541-025-01319-2
  • Primary Citation of Related Structures:  
    9LU3, 9LUE

  • PubMed Abstract: 

    Nipah virus (NiV) and Hendra virus (HeV), two highly pathogenic Henipaviruses (HNVs), pose a significant public health threat. The attachment glycoprotein (G) plays a crucial role in viral attachment and entry, making it an attractive target for vaccine and therapeutic antibody development. However, the antigenic landscape and neutralization sensitivity of the diverse HNV G proteins remain poorly defined. Here, we systematically characterize 27 monoclonal antibodies (mAbs) elicited by NiV G head (G H ) nanoparticle-immunized mice. Among these, 25 mAbs exhibit neutralizing activity against two major NiV strains, NiV-Malaysia and NiV-Bangladesh, with five mAbs also cross-inhibiting HeV infection. Notably, mAbs from two distinct groups conferred complete protection to hamsters against lethal NiV-Malaysia challenge. Structural analysis of NiV G H in complex with representative Fabs reveals four non-overlapping epitopes, including two novel antigenic sites and one public protective epitope shared across species. MAbs targeting the novel sites bind to the top or side faces of G protein's β-propeller and inhibit viral infection by blocking either receptor engagement or membrane fusion. MAbs recognizing the public epitope block the receptor binding directly. Our study provides a comprehensive antigenic map of the NiV G H and offers new insights and opportunities for antibody-based therapies and rational vaccine development.


  • 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
Glycoprotein GA,
D [auth B]
441Henipavirus nipahenseMutation(s): 0 
UniProt
Find proteins for Q9IH62 (Nipah virus)
Explore Q9IH62 
Go to UniProtKB:  Q9IH62
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9IH62
Glycosylation
Glycosylation Sites: 5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
mAb LN1F9 Fab heavy chainB [auth H],
E [auth D]
234Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
mAb LN1F9 Fab light chainC [auth L],
F [auth E]
214Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.269 (Depositor), 0.268 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.416α = 90
b = 125.155β = 90
c = 152.376γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-26
    Type: Initial release
  • Version 1.1: 2025-12-10
    Changes: Database references