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- EMDB-26662: Prefusion-stabilized Nipah virus fusion protein complexed with Fa... -

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Basic information

Entry
Database: EMDB / ID: EMD-26662
TitlePrefusion-stabilized Nipah virus fusion protein complexed with Fab 2B12
Map dataPrefusion-stabilized Nipah virus fusion protein complexed with Fab 2B12
Sample
  • Complex: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2B12
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: Fab 2B12 heavy chain
    • Protein or peptide: Fab 2B12 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHenipavirus / Nipah virus / NiV / F / fusion / prefusion / preF / pre-F / neutralizing antibody / Fab / 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 speciesNipah henipavirus / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsByrne PO / McLellan JS
Funding support United States, 1 items
OrganizationGrant numberCountry
Welch FoundationF-0003-19620604 United States
CitationJournal: Nat Commun / Year: 2023
Title: Structural basis for antibody recognition of vulnerable epitopes on Nipah virus F protein.
Authors: Patrick O Byrne / Brian E Fisher / David R Ambrozak / Elizabeth G Blade / Yaroslav Tsybovsky / Barney S Graham / Jason S McLellan / Rebecca J Loomis /
Abstract: Nipah virus (NiV) is a pathogenic paramyxovirus that causes fatal encephalitis in humans. Two envelope glycoproteins, the attachment protein (G/RBP) and fusion protein (F), facilitate entry into host ...Nipah virus (NiV) is a pathogenic paramyxovirus that causes fatal encephalitis in humans. Two envelope glycoproteins, the attachment protein (G/RBP) and fusion protein (F), facilitate entry into host cells. Due to its vital role, NiV F presents an attractive target for developing vaccines and therapeutics. Several neutralization-sensitive epitopes on the NiV F apex have been described, however the antigenicity of most of the F protein's surface remains uncharacterized. Here, we immunize mice with prefusion-stabilized NiV F and isolate ten monoclonal antibodies that neutralize pseudotyped virus. Cryo-electron microscopy reveals eight neutralization-sensitive epitopes on NiV F, four of which have not previously been described. Novel sites span the lateral and basal faces of NiV F, expanding the known library of vulnerable epitopes. Seven of ten antibodies bind the Hendra virus (HeV) F protein. Multiple sequence alignment suggests that some of these newly identified neutralizing antibodies may also bind F proteins across the Henipavirus genus. This work identifies new epitopes as targets for therapeutics, provides a molecular basis for NiV neutralization, and lays a foundation for development of new cross-reactive antibodies targeting Henipavirus F proteins.
History
DepositionApr 14, 2022-
Header (metadata) releaseMar 29, 2023-
Map releaseMar 29, 2023-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26662.png

Downloads & links

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Map

FileDownload / File: emd_26662.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrefusion-stabilized Nipah virus fusion protein complexed with Fab 2B12
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 540 pix.
= 356.4 Å		0.66 Å/pix.
x 540 pix.
= 356.4 Å		0.66 Å/pix.
x 540 pix.
= 356.4 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.2
Minimum - Maximum-5.777853 - 10.693337
Average (Standard dev.)-0.0006123207 (±0.24468605)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 356.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_26662_msk_1.map
Projections & Slices
AxesZYX

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Additional map: Additional map 1

Fileemd_26662_additional_1.map
AnnotationAdditional map 1
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Half map: Half Map 1

Fileemd_26662_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_26662_half_map_2.map
AnnotationHalf Map 2
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Sample components

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Entire : Prefusion-stabilized Nipah virus fusion protein complexed with Fa...

EntireName: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2B12
Components
  • Complex: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2B12
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: Fab 2B12 heavy chain
    • Protein or peptide: Fab 2B12 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Prefusion-stabilized Nipah virus fusion protein complexed with Fa...

SupramoleculeName: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2B12
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Nipah henipavirus

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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: Nipah henipavirus
Molecular weightTheoretical: 52.165996 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVVILDKRCY CNLLILILMI SECSVGILHY EKLSKIGLVK GVTRKYKIKS NPLTKDIVIK MIPNVSNMSQ CTGSVMENYK TRLNGILTP IKGALEIYKN NTHDCVGDVR LAGVCMAGVA IGIATAAQIT AGVALYEAMK NADNINKLKS SIESTNEAVV K LQETAEKT ...String:
MVVILDKRCY CNLLILILMI SECSVGILHY EKLSKIGLVK GVTRKYKIKS NPLTKDIVIK MIPNVSNMSQ CTGSVMENYK TRLNGILTP IKGALEIYKN NTHDCVGDVR LAGVCMAGVA IGIATAAQIT AGVALYEAMK NADNINKLKS SIESTNEAVV K LQETAEKT VYVFTALQDY INTNLVPTID KIPCKQTELS LDLALSKYLS DLLFVFGPNL QDPVSNSMTI QAISQAFGGN YE TLLRTLG YATEDFDDLL ESDSITGQII YVDLSSYYII VRVYFPILTE IQQAYIQELL PVSFNNDNSE WISIVPNFIL VRN TLISNI EIGFCLITKR SVICNQDYAT PMTNNMRECL TGSTEKCPRE LVVSSHVPRF ALSNGVLFAN CISVTCQCQT TGRA ISQSG EQTLLMIDNT TCPTAVLGNV IISLGKYLGS VNYNSEGIAI GPPVFTDKVD ISSQISSMNQ SLQQSKDYI

UniProtKB: Fusion glycoprotein F0

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Macromolecule #2: Fab 2B12 heavy chain

MacromoleculeName: Fab 2B12 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 15.521596 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MEFGLSWIFL AAILKGVQCE VQLVESGGGL VQPKGSLKLS CAASGFIFNT YAMHWVRQAP GKGLEWVARI RSKSSNYATY YADSVKDRF TISRDDSQSM LYLQMNNLKT EDTAMYYCVR EGGYYFDYWG QGTTLTVSA

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Macromolecule #3: Fab 2B12 light chain

MacromoleculeName: Fab 2B12 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 14.608595 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MEFGLSWIFL AAILKGVQCD IVMSQSPSSL AVSVGEKVTM SCKSSQSLLH VSNQKNYLAW YQQKPGQSPK LLIYWASTRE SGVPDRFTG SGSGTDFTLT ISSVKAEDLA VYYCQQYYSY PWPFGGGTKL EIK

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 12 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 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 reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 694547
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD

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