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- PDB-9ua9: Nipah virus fusion glycoprotein in complex with a broadly neutral... -

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Basic information

Entry
Database: PDB / ID: 9ua9
TitleNipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 1D6
Components
  • 1D6 VH
  • 1D6-VL
  • Fusion glycoprotein F0
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Henipavirus / Fusion glycoprotein / Antibody / ANTIVIRAL PROTEIN / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0
Similarity search - Domain/homology
Fusion glycoprotein F0
Similarity search - Component
Biological speciesMacaca (macaques)
Henipavirus nipahense
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.99 Å
AuthorsFan, P.F. / Ren, Y. / Yu, C.M. / Chen, W.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentJCKY2020802B001 China
CitationJournal: Adv Sci (Weinh) / Year: 2025
Title: Potent Cross-neutralizing Antibodies Reveal Vulnerabilities of Henipavirus Fusion Glycoprotein.
Authors: Yi Ren / Pengfei Fan / Xinghai Zhang / Ting Fang / Zhengshan Chen / Yanfeng Yao / Xiangyang Chi / Guanying Zhang / Xiaofan Zhao / Bingjie Sun / Fangxu Li / Zixuan Liu / Zhenwei Song / Baoyue ...Authors: Yi Ren / Pengfei Fan / Xinghai Zhang / Ting Fang / Zhengshan Chen / Yanfeng Yao / Xiangyang Chi / Guanying Zhang / Xiaofan Zhao / Bingjie Sun / Fangxu Li / Zixuan Liu / Zhenwei Song / Baoyue Zhang / Cheng Peng / Entao Li / Yilong Yang / Jianmin Li / Sandra Chiu / Changming Yu /
Abstract: Hendra and Nipah viruses (HNVs), zoonotic paramyxoviruses with >50% case fatality rates, cause fatal encephalitis and respiratory disease, yet lack approved therapies. Here, nine rhesus-derived ...Hendra and Nipah viruses (HNVs), zoonotic paramyxoviruses with >50% case fatality rates, cause fatal encephalitis and respiratory disease, yet lack approved therapies. Here, nine rhesus-derived monoclonal antibodies (mAbs) targeting the fusion glycoprotein (F) prefusion conformation are developed. Four mAbs exhibit first-rate cross-neutralization against HNVs, with two showing synergistic potency when combined with attachment glycoprotein (G)-specific mAbs. Single-dose administration of mAbs confers robust protection against lethal Nipah virus challenge in hamsters. Structural insights reveal that 8 of the 9 potent mAbs adopt a human IGHV4-59-like framework with protruding CDRH3 loops, forming pushpin-shaped paratopes that stabilize the prefusion F-trimer by occupying vulnerable interprotomer cavities. Systematic mutational profiling identifies 14 prefusion-locking residues within the F ectodomain, classified as i) structural linchpins governing fusogenicity or ii) immunodominant hotspots targeted by cross-neutralizing mAbs. This work delivers promising therapeutic candidates against HNVs and provides blueprints for the rational design of antibodies and vaccines targeting viral fusion machinery.
History
DepositionMar 31, 2025Deposition site: PDBJ / Processing site: PDBJ
SupersessionApr 9, 2025ID: 8XN9
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Apr 9, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: 1D6-VL
H: 1D6 VH
A: Fusion glycoprotein F0
C: Fusion glycoprotein F0
B: Fusion glycoprotein F0
G: 1D6 VH
I: 1D6 VH
E: 1D6-VL
D: 1D6-VL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,49721
Polymers223,2339
Non-polymers3,26412
Water9,962553
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Antibody , 2 types, 6 molecules FEDHGI

#1: Antibody 1D6-VL


Mass: 11247.248 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca (macaques) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody 1D6 VH


Mass: 13690.283 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca (macaques) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)

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Protein / Non-polymers , 2 types, 556 molecules ACB

#3: Protein Fusion glycoprotein F0 / Protein F


Mass: 49473.598 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Henipavirus nipahense / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: Q9IH63
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 553 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 12 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: 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.: 9 / 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

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Nipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 1D6COMPLEX#1-#30RECOMBINANT
2Nipah virus fusion glycoproteinCOMPLEX#31RECOMBINANT
31D6 VHCOMPLEX#21RECOMBINANT
41D6 VLCOMPLEX#11RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
32Henipavirus nipahense3052225
43Macaca (macaques)9539
54Macaca (macaques)9539
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
22Homo sapiens (human)9606Expi293
43Homo sapiens (human)9606Expi293
54Homo sapiens (human)9606Expi293
Buffer solutionpH: 7.4 / Details: 137 mM NaCl, 2.7mM KCl, 10 mM Na2HPO4, 2 mM KH2PO4
SpecimenConc.: 0.03 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 47.51 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19.2_4158: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 1.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1141629 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00216089
ELECTRON MICROSCOPYf_angle_d0.53621891
ELECTRON MICROSCOPYf_dihedral_angle_d11.6215871
ELECTRON MICROSCOPYf_chiral_restr0.0462625
ELECTRON MICROSCOPYf_plane_restr0.0042766

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