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- EMDB-45622: Fab fragment of Antibody with NiV glycoprotein F -

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Basic information

Entry
Database: EMDB / ID: EMD-45622
TitleFab fragment of Antibody with NiV glycoprotein F
Map dataFile exported as .mrc at contour 0.18 and pixel spacing 0.825 from session. Sharpened map using DeepEMhancer
Sample
  • Complex: Fab fragment with NiV F0 fusion protein
    • Protein or peptide: Antibody Heavy Chain
    • Protein or peptide: Antibody Light Chain
    • Protein or peptide: Fusion glycoprotein F0
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsFusion complex antibody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homologymembrane fusion involved in viral entry into host cell / Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / Fusion glycoprotein F0
Function and homology information
Biological speciesHenipavirus nipahense / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsOuizougun-Oubari M / Bajic G
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Transl Med / Year: 2026
Title: A cocktail of human mAbs targeting the henipavirus fusion and receptor binding proteins provides cross-species neutralization.
Authors: Axel A Guzmán-Solís / Mohamed Ouizougun-Oubari / Olivier Escaffre / Brendan B Larsen / Mary Lopez / Selina Locklear / Madhu Kumar / Terry L Juelich / Jennifer K Smith / Lihong Zhang / ...Authors: Axel A Guzmán-Solís / Mohamed Ouizougun-Oubari / Olivier Escaffre / Brendan B Larsen / Mary Lopez / Selina Locklear / Madhu Kumar / Terry L Juelich / Jennifer K Smith / Lihong Zhang / Griffin D Haas / Rachel Roenicke / Luca Brambilla / Kasopefoluwa Y Oguntuyo / Aum R Patel / Iden A Sapse / Thomas A Bowden / Domenico Tortorella / Jesse D Bloom / Alexander N Freiberg / Goran Bajic / James Andrew Duty / Benhur Lee /
Abstract: The Nipah and Hendra viruses (NiV and HeV, respectively) are highly pathogenic, with case fatality rates of 40 to 75%, representing substantial public health threats. Although one monoclonal antibody ...The Nipah and Hendra viruses (NiV and HeV, respectively) are highly pathogenic, with case fatality rates of 40 to 75%, representing substantial public health threats. Although one monoclonal antibody (mAb), mAb102.4, has advanced through phase 1 clinical trials, there remains a critical need for approved therapeutic options against these henipaviruses (HNVs). Development of human mAbs has been constrained by limited access to convalescent patient samples. Here, we describe human mAbs derived from transgenic humanized mice that cross-neutralize extant NiV and HeV strains by binding to their fusion protein (F) or receptor binding protein (RBP). Deep mutational scanning and functional studies demonstrated that the anti-RBP mAb (8G3) targets the receptor binding site and requires multiple simultaneous mutations for escape. Sequence analysis of our anti-F mAbs identified a clonally expanded VH3-33 family with evidence of somatic hypermutation, yielding high-affinity antibodies. Cryo-electron microscopy revealed that our most potent F antibody (2A1) recognizes a conserved quaternary epitope spanning two protomers in trimeric prefusion NiV-F and stabilized, rather than displaced, a key glycan shield, distinguishing it from previously described antibodies targeting this region. The 8G3 and 2A1 mAbs exhibited additive neutralization when combined and provided complete protection against lethal NiV challenge in hamsters when administered individually or as a cocktail, even when treatment was delayed. Using a pseudovirus system, we show that this dual-targeting approach was resilient against a suite of escape mutants compared with monotherapy. Our findings establish a candidate therapeutic strategy that minimizes development of resistance, providing a foundation for next-generation countermeasures against emerging HNVs.
History
DepositionJul 3, 2024-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45622.png

Downloads & links

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Map

FileDownload / File: emd_45622.map.gz / Format: CCP4 / Size: 142.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFile exported as .mrc at contour 0.18 and pixel spacing 0.825 from session. Sharpened map using DeepEMhancer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 334 pix.
= 275.55 Å		0.83 Å/pix.
x 334 pix.
= 275.55 Å		0.83 Å/pix.
x 334 pix.
= 275.55 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.0017820997 - 1.6687081
Average (Standard dev.)0.0021097327 (±0.03189735)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions334334334
Spacing334334334
CellA=B=C: 275.55 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: File exported as .mrc at contour 0.18 and...

Fileemd_45622_additional_1.map
AnnotationFile exported as .mrc at contour 0.18 and pixel spacing 0.825 from session
Projections & Slices
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Half map: Map half A cont 0.18

Fileemd_45622_half_map_1.map
AnnotationMap_half_A cont 0.18
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Map half B cont 0.18

Fileemd_45622_half_map_2.map
AnnotationMap_half_B cont 0.18
Projections & Slices
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Sample components

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Entire : Fab fragment with NiV F0 fusion protein

EntireName: Fab fragment with NiV F0 fusion protein
Components
  • Complex: Fab fragment with NiV F0 fusion protein
    • Protein or peptide: Antibody Heavy Chain
    • Protein or peptide: Antibody Light Chain
    • Protein or peptide: Fusion glycoprotein F0
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Fab fragment with NiV F0 fusion protein

SupramoleculeName: Fab fragment with NiV F0 fusion protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#3, #1
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: 60.666555 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGILPSPGMP ALLSLVSLLS VLLMGCVAET GGILHYEKLS KIGLVKGVTR KYKIKSNPLT KDIVIKMIPN VSNMSQCTGS VMENYKTRL NGILTPIKGA LEIYKNNTHD CVGDVRLAGV CMAGVAIGIA TAAQITAGVA LYEAMKNADN INKLKSSIES T NEAVVKLQ ...String:
MGILPSPGMP ALLSLVSLLS VLLMGCVAET GGILHYEKLS KIGLVKGVTR KYKIKSNPLT KDIVIKMIPN VSNMSQCTGS VMENYKTRL NGILTPIKGA LEIYKNNTHD CVGDVRLAGV CMAGVAIGIA TAAQITAGVA LYEAMKNADN INKLKSSIES T NEAVVKLQ ETAEKTVYVF TALQDYINTN LVPTIDKIPC KQTELSLDLA LSKYLSDLLF VFGPNLQDPV SNSMTIQAIS QA FGGNYET LLRTLGYATE DFDDLLESDS ITGQIIYVDL SSYYIIVRVY FPILTEIQQA YIQELLPVSF NNDNSEWISI VPN FILVRN TLISNIEIGF CLITKRSVIC NQDYATPMTN NMRECLTGST EKCPRELVVS SHVPRFALSN GVLFANCISV TCQC QTTGR AISQSGEQTL LMIDNTTCPT AVLGNVIISL GKYLGSVNYN SEGIAIGPPV FTDKVDISSQ ISSMNQSLQQ SKDYI KEAQ RLLDGTMKQI EDKIEEILSK IYHIENEIAR IKKLIGEGGS GGSGLNDIFE AQKIEWHEGR TKHHHHHH

UniProtKB: Fusion glycoprotein F0

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Macromolecule #2: Antibody Heavy Chain

MacromoleculeName: Antibody Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.464017 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVESGGG VVQPGRSLRL SCAASGFTFS SYGIHWVRQA PGKGLEWVAL IDYAGSNKYY SDSVKGRFTI SRDNSKNTLY LQMKSLRAE DTAVYYCARD RDYGILTGYP DYWGQGALVT VSS

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Macromolecule #3: Antibody Light Chain

MacromoleculeName: Antibody Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.568906 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
IVLTQSPATL SLSPGERATL SCRASQSVSS YLAWYQQKPG QAPRLLIYDA SNRATGIPAR FSGSGSGTDF TLTISSLEPE DFAVYYCQH RSNWPPLTFG GGTKVEIK

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 6 / 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.44 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 135929
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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