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- PDB-9lu3: LN1F9 Fab bound to Nipah Virus attachment (G) glycoprotein head domain -

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Basic information

Entry
Database: PDB / ID: 9lu3
TitleLN1F9 Fab bound to Nipah Virus attachment (G) glycoprotein head domain
Components
  • Glycoprotein G
  • mAb LN1F9 Fab heavy chain
  • mAb LN1F9 Fab light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Glycoprotein G / Fab / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / exo-alpha-sialidase activity / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / identical protein binding / membrane
Similarity search - Function
Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesHenipavirus nipahense
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDeng, Z. / Kuang, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: NPJ Vaccines / Year: 2025
Title: Antigenic landscape of Nipah virus attachment glycoprotein analysis reveals a protective immunodominant epitope across species.
Authors: Dan Zhou / Yong Wang / Yanfeng Yao / Wenhua Kuang / Rao Cheng / Gan Zhang / Hang Liu / Xin Li / Sandra Chiu / Zengqin Deng / Haiyan Zhao /
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 ...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) 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 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 and offers new insights and opportunities for antibody-based therapies and rational vaccine development.
History
DepositionFeb 7, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2025Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoprotein G
H: mAb LN1F9 Fab heavy chain
L: mAb LN1F9 Fab light chain
B: Glycoprotein G
D: mAb LN1F9 Fab heavy chain
E: mAb LN1F9 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,63916
Polymers196,4276
Non-polymers2,21210
Water00
1
A: Glycoprotein G
hetero molecules

D: mAb LN1F9 Fab heavy chain
E: mAb LN1F9 Fab light chain


Theoretical massNumber of molelcules
Total (without water)99,3208
Polymers98,2133
Non-polymers1,1065
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_544-x,y-1/2,-z-1/21
Buried area6630 Å2
ΔGint-16 kcal/mol
Surface area34730 Å2
MethodPISA
2
B: Glycoprotein G
hetero molecules

H: mAb LN1F9 Fab heavy chain
L: mAb LN1F9 Fab light chain


Theoretical massNumber of molelcules
Total (without water)99,3208
Polymers98,2133
Non-polymers1,1065
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y+1/2,-z+1/21
Buried area6820 Å2
ΔGint-15 kcal/mol
Surface area35160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.416, 125.155, 152.376
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Glycoprotein G


Mass: 49608.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Henipavirus nipahense / Production host: Homo (humans) / References: UniProt: Q9IH62
#2: Antibody mAb LN1F9 Fab heavy chain


Mass: 25208.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody mAb LN1F9 Fab light chain


Mass: 23396.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 58.94 %
Crystal growTemperature: 289 K / Method: evaporation
Details: 0.3 M ammonium formate, 0.1 M HEPES pH 7.0, 20 % [vol/vol] Sokalan CP5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3→28.6 Å / Num. obs: 47546 / % possible obs: 99.1 % / Redundancy: 5.2 % / CC1/2: 0.983 / Rmerge(I) obs: 0.128 / Net I/σ(I): 5.6
Reflection shellResolution: 3→3.1 Å / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4516 / CC1/2: 0.754

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→20.44 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2688 2373 5.05 %
Rwork0.2194 --
obs0.2219 46949 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→20.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13193 0 140 0 13333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01113647
X-RAY DIFFRACTIONf_angle_d1.32618558
X-RAY DIFFRACTIONf_dihedral_angle_d7.1981896
X-RAY DIFFRACTIONf_chiral_restr0.0682105
X-RAY DIFFRACTIONf_plane_restr0.0122362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.060.40221390.33222530X-RAY DIFFRACTION96
3.06-3.130.35721320.33162599X-RAY DIFFRACTION99
3.13-3.20.41811430.30432568X-RAY DIFFRACTION98
3.2-3.280.3381250.29662613X-RAY DIFFRACTION99
3.28-3.370.38361480.2942607X-RAY DIFFRACTION99
3.37-3.470.37911350.2772595X-RAY DIFFRACTION98
3.47-3.580.29581460.26792577X-RAY DIFFRACTION98
3.58-3.710.31551330.25052561X-RAY DIFFRACTION97
3.71-3.850.2961240.23412626X-RAY DIFFRACTION99
3.85-4.030.27421540.22342596X-RAY DIFFRACTION99
4.03-4.240.2211410.20172622X-RAY DIFFRACTION99
4.24-4.50.21451510.17312621X-RAY DIFFRACTION98
4.5-4.840.21061420.17252627X-RAY DIFFRACTION99
4.84-5.320.23141360.17662684X-RAY DIFFRACTION99
5.32-6.080.24631600.19312644X-RAY DIFFRACTION99
6.08-7.590.23571380.20022720X-RAY DIFFRACTION99
7.59-20.440.19511260.16912786X-RAY DIFFRACTION98

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