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- EMDB-63235: An antibody target the fusion protein of Nipah virus -

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Basic information

Entry
Database: EMDB / ID: EMD-63235
TitleAn antibody target the fusion protein of Nipah virus
Map data
Sample
  • Complex: Complex of Nipah virus fusion protein with an antibody
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: Fab NiF03-3C9 heavy chain
    • Protein or peptide: Fab NiF03-3C9 light chain
KeywordsNipah virus / antibody / complex / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / 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 / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.45 Å
AuthorsXu H / Su XD
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFC2301402 China
CitationJournal: Antiviral Res / Year: 2025
Title: A monoclonal antibody targeting conserved regions of pre-fusion protein cross-neutralizes Nipah and Hendra virus variants.
Authors: Tao Li / Hua Xu / Mengyi Zhang / Jianhui Nie / Binfan Liao / Jingshu Xie / Yinan Jiang / Yawen Liu / Pingju Ge / Chunhui Zhao / Ziqi Sun / Yunbo Bai / Maoling Tang / Xiaodong Su / Youchun Wang / Weijin Huang /
Abstract: Nipah virus (NiV) and Hendra virus (HeV) have an extremely high case fatality, leading to hundreds of deaths in several countries around the globe. Belonging to the same genus Henipavirus (HNV), the ...Nipah virus (NiV) and Hendra virus (HeV) have an extremely high case fatality, leading to hundreds of deaths in several countries around the globe. Belonging to the same genus Henipavirus (HNV), the two species have a high degree of sequence similarity, resulting in cross-neutralizing immunity under favorable conditions. Here, we obtained ten anti-NiV-F monoclonal antibodies using hybridoma technology, and verified that these antibodies had potent neutralizing activities against epidemic NiV strains from different regions using a pseudovirus assay, and the neutralizing concentration reached the nanogram per milliliter level. Moreover, two of the antibodies, NiF03-3C9 and NiF03-2F6, were found to have cross-neutralizing activity against HeV, which was even stronger than that against NiV. Epitope competition analysis revealed two classes of epitopes for these antibodies. Cryo-electron microscopy showed that NiF03-3C9 binds to lateral residues of the prefusion F protein trimer, highly conserved in both Nipah and Hendra. The protective potency of the antibodies was also validated using in vivo pseudovirus infection models of Nipah and Hendra viruses. The mAbs developed in this study and their conserved cross-neutralizing epitopes elucidated by structural analysis may contribute to the control of highly pathogenic HNV outbreaks.
History
DepositionJan 21, 2025-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63235.png

Downloads & links

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Map

FileDownload / File: emd_63235.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-2.2325845 - 3.3613236
Average (Standard dev.)0.0011206213 (±0.10377874)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_63235_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63235_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of Nipah virus fusion protein with an antibody

EntireName: Complex of Nipah virus fusion protein with an antibody
Components
  • Complex: Complex of Nipah virus fusion protein with an antibody
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: Fab NiF03-3C9 heavy chain
    • Protein or peptide: Fab NiF03-3C9 light chain

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Supramolecule #1: Complex of Nipah virus fusion protein with an antibody

SupramoleculeName: Complex of Nipah virus fusion protein with an antibody
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Henipavirus nipahense

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Macromolecule #1: Fusion glycoprotein F0

MacromoleculeName: Fusion glycoprotein F0 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Henipavirus nipahense
Molecular weightTheoretical: 54.739805 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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 DYIKEAQRLL DTVNPSLKLM KQIEDKIEEI LSKIY HIEN EIARIKKLIG E

UniProtKB: Fusion glycoprotein F0

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Macromolecule #2: Fab NiF03-3C9 heavy chain

MacromoleculeName: Fab NiF03-3C9 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.750713 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLQQSGPE LVKPGASMKI ACKASGYSFT DYTMNWVKQS HGKNLEWIGL INPYIGGTNY NQKFKGKATL TVDKSSSTAY MELLSLTFE DSAVYYCARD PSRAMDYWGQ GTSVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY FPEPVTVSWN S GALTSGVH ...String:
EVQLQQSGPE LVKPGASMKI ACKASGYSFT DYTMNWVKQS HGKNLEWIGL INPYIGGTNY NQKFKGKATL TVDKSSSTAY MELLSLTFE DSAVYYCARD PSRAMDYWGQ GTSVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY FPEPVTVSWN S GALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK SCDK

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Macromolecule #3: Fab NiF03-3C9 light chain

MacromoleculeName: Fab NiF03-3C9 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.229797 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPAS LSASVGETVT ITCGASENIY GALNWFQRKQ GKSPQLLIYG ATNLADGMSS RFSGSGSGRQ YSLKIGSMHP DDVATYYCQ NVLSTPWTFG GGTRLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPAS LSASVGETVT ITCGASENIY GALNWFQRKQ GKSPQLLIYG ATNLADGMSS RFSGSGSGRQ YSLKIGSMHP DDVATYYCQ NVLSTPWTFG GGTRLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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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

Concentration0.4 mg/mL
BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 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: 2.45 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 477578
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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