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- EMDB-63982: Nipah virus fusion glycoprotein in complex with a broadly neutral... -

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Basic information

Entry
Database: EMDB / ID: EMD-63982
TitleNipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 1D6
Map data
Sample
  • Complex: Nipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 1D6
    • Complex: Nipah virus fusion glycoprotein
      • Protein or peptide: Fusion glycoprotein F0
    • Complex: 1D6 VH
      • Protein or peptide: 1D6 VH
    • Complex: 1D6 VL
      • Protein or peptide: 1D6-VL
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
KeywordsHenipavirus / 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 speciesHenipavirus nipahense / Macaca (macaques)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.99 Å
AuthorsFan PF / Ren Y / Yu CM / Chen W
Funding support China, 1 items
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, 2025-
SupersessionApr 9, 2025ID: EMD-38499
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63982.png

Downloads & links

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Map

FileDownload / File: emd_63982.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 460 pix.
= 340.4 Å		0.74 Å/pix.
x 460 pix.
= 340.4 Å		0.74 Å/pix.
x 460 pix.
= 340.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.188
Minimum - Maximum-1.9812429 - 4.226046
Average (Standard dev.)0.00001417722 (±0.08051938)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 340.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63982_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63982_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Nipah virus fusion glycoprotein in complex with a broadly neutral...

EntireName: Nipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 1D6
Components
  • Complex: Nipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 1D6
    • Complex: Nipah virus fusion glycoprotein
      • Protein or peptide: Fusion glycoprotein F0
    • Complex: 1D6 VH
      • Protein or peptide: 1D6 VH
    • Complex: 1D6 VL
      • Protein or peptide: 1D6-VL
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: Nipah virus fusion glycoprotein in complex with a broadly neutral...

SupramoleculeName: Nipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 1D6
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: Nipah virus fusion glycoprotein

SupramoleculeName: Nipah virus fusion glycoprotein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Henipavirus nipahense

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Supramolecule #3: 1D6 VH

SupramoleculeName: 1D6 VH / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Macaca (macaques)

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Supramolecule #4: 1D6 VL

SupramoleculeName: 1D6 VL / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Macaca (macaques)

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Macromolecule #1: 1D6-VL

MacromoleculeName: 1D6-VL / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca (macaques)
Molecular weightTheoretical: 11.247248 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
PVLTQPPSAS EAARKSVTIS CSGSSSNIGS NSVSWYQQLP GTALKLLISY NDQRASGVSD RFSGSKSGTS ASLAISGLQT EDEADYYCA AWDDSLSGPV FGGGTRLTVL

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Macromolecule #2: 1D6 VH

MacromoleculeName: 1D6 VH / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca (macaques)
Molecular weightTheoretical: 13.690283 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGPG LVKPSETLSL TCTVSGASIS SYWWGWIRQP PGKGLEWIAD IYPNSGSTNY NPSLKSRVTN SKDASKNQFS LKLSSVTAA DTAMYYCARA PRGYSYSYVF GHRFDVWGPG VLVTVS

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Macromolecule #3: Fusion glycoprotein F0

MacromoleculeName: Fusion glycoprotein F0 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Henipavirus nipahense
Molecular weightTheoretical: 49.473598 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ILHYEKLSKI GLVKGVTRKY KIKSNPLTKD IVIKMIPNVS NMSQCTGSVM ENYKTRLNGI LTPIKGALEI YKNNTHDLVG DVRLAGVIM AGVAIGIATA AQITAGVALY EAMKNADNIN KLKSSIESTN EAVVKLQETA EKTVYVLTAL QDYINTNLVP T IDKISCKQ ...String:
ILHYEKLSKI GLVKGVTRKY KIKSNPLTKD IVIKMIPNVS NMSQCTGSVM ENYKTRLNGI LTPIKGALEI YKNNTHDLVG DVRLAGVIM AGVAIGIATA AQITAGVALY EAMKNADNIN KLKSSIESTN EAVVKLQETA EKTVYVLTAL QDYINTNLVP T IDKISCKQ TELSLDLALS KYLSDLLFVF GPNLQDPVSN SMTIQAISQA FGGNYETLLR TLGYATEDFD DLLESDSITG QI IYVDLSS YYIIVRVYFP ILTEIQQAYI QELLPVSFNN DNSEWISIVP NFILVRNTLI SNIEIGFCLI TKRSVICNQD YAT PMTNNM RECLTGSTEK CPRELVVSSH VPRFALSNGV LFANCISVTC QCQTTGRAIS QSGEQTLLMI DNTTCPTAVL GNVI ISLGK YLGSVNYNSE GIAIGPPVFT DKVDISSQIS SMNQSLQQSK DYIKE

UniProtKB: Fusion glycoprotein F0

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 9 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 553 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.03 mg/mL
BufferpH: 7.4 / Details: 137 mM NaCl, 2.7mM KCl, 10 mM Na2HPO4, 2 mM KH2PO4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 47.51 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.4 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.99 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1141629
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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