9LUE | pdb_00009lue

Cryo-EM structure of the Nipah G head domain in complex with three Fabs


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.03 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.2 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 11: 5-5

  • DOI: https://doi.org/10.1038/s41541-025-01319-2
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 124.87 kDa 
  • Atom Count: 8,693 
  • Modeled Residue Count: 1,099 
  • Deposited Residue Count: 1,108 
  • Unique protein chains: 7

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycoprotein GA [auth G]426Henipavirus 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
NIV LN3D3 Fab Light ChainB [auth L]107Mesocricetus auratusMutation(s): 0 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
NiV S2B10 Fab Heavy ChainC [auth A]119Mesocricetus auratusMutation(s): 0 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
NiV S2B10 Fab Light ChainD [auth B]111Mesocricetus auratusMutation(s): 0 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
NiV S1E2 Fab Heavy ChainE [auth C]120Mesocricetus auratusMutation(s): 0 
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
NiV S1E2 Fab Light ChainF [auth D]106Mesocricetus auratusMutation(s): 0 
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
NIV LN3D3 Fab Heavy ChainG [auth H]119Mesocricetus auratusMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.03 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONCoot

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: 2025-11-26
    Type: Initial release
  • Version 1.1: 2025-12-10
    Changes: Data collection, Database references
  • Version 1.2: 2026-01-21
    Changes: Data collection, Database references