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- EMDB-48715: Cryo-EM map of vaccine elicited antibody 22F5 bound to post-fusio... -

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Basic information

Entry
Database: EMDB / ID: EMD-48715
TitleCryo-EM map of vaccine elicited antibody 22F5 bound to post-fusion conformation of Langya virus F protein
Map dataSharpened map
Sample
  • Complex: Vaccine elicted antibody 22F5 bound to post-fusion conformation of Langya virus F protein
    • Complex: Langya virus F protein
    • Complex: 22F5 Fab
KeywordsHenipavirus / Langya virus / vaccine-elicited antibody / DII domain / shrew-origin / ANTIVIRAL PROTEIN
Function / homologyPrecursor 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 speciesLangya virus / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.31 Å
AuthorsKumar U / Acharya P
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat Commun / Year: 2026
Title: Mechanistic and antigenic boundaries of Henipavirus and Parahenipavirus glycoproteins.
Authors: Aaron J May / Muralikrishna Lella / Jared Lindenberger / Alex Berkman / Ujjwal Kumar / Kejun Liu / Moumita Dutta / Maggie Barr / Rob Parks / Xiaozhi Lu / Madison Berry / Amanda Powell / ...Authors: Aaron J May / Muralikrishna Lella / Jared Lindenberger / Alex Berkman / Ujjwal Kumar / Kejun Liu / Moumita Dutta / Maggie Barr / Rob Parks / Xiaozhi Lu / Madison Berry / Amanda Powell / Amelia G Thompson / Sravya Sowdamini Nakka / Camila T França / Xiao Huang / Arpita Mrigwani / Kijun Song / Victor Ilevbare / Salam Sammour / Chan Soo Park / Radha Devkota Adhikari / Priyanka Devkota / Katarzyna Janowska / Yanshun Liu / Garrett Scapellato / Taylor N Spence / Katayoun Mansouri / Kevin Wiehe / Nancy J Sullivan / Rosemarie Mason / Robert J Edwards / Kevin O Saunders / Barton F Haynes / Priyamvada Acharya /
Abstract: Henipaviruses, in the Paramyxoviridae family, includes the highly virulent Nipah virus that causes reoccurring outbreaks of deadly disease. Recent discoveries of Henipavirus-like species, including ...Henipaviruses, in the Paramyxoviridae family, includes the highly virulent Nipah virus that causes reoccurring outbreaks of deadly disease. Recent discoveries of Henipavirus-like species, including the zoonotic Langya virus, have revealed much higher antigenic diversity than currently characterized and prompted the reorganization of these viruses into the Henipavirus and Parahenipavirus genera. Here, to explore the limits of structural and antigenic variation in both genera, collectively referred to as HNVs, we construct an expanded, diverse panel of HNV fusion and attachment glycoproteins from non-redundant HNV strains that better reflect global HNV diversity. We express and purify the fusion protein ectodomains and the attachment protein head domains and study their biochemical and biophysical properties. We perform immunization experiments in mice, eliciting antibodies reactive to multiple HNV fusion proteins. Cryo-electron microscopy structures elucidate molecular determinants of differential pre-fusion state stability and higher order contacts. A crystal structure of the Gamak virus attachment head domain reveals an additional domain appended to the conserved 6-bladed, β-propeller fold. Taken together, these studies expand the known structural and antigenic limits of the HNVs, reveal cross-reactive epitopes within both genera and provide foundational data for the development of broadly reactive countermeasures.
History
DepositionJan 19, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48715.png

Downloads & links

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Map

FileDownload / File: emd_48715.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.186
Minimum - Maximum-1.8013783 - 2.3585498
Average (Standard dev.)-0.0006292171 (±0.04031596)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 352.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_48715_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_48715_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Vaccine elicted antibody 22F5 bound to post-fusion conformation o...

EntireName: Vaccine elicted antibody 22F5 bound to post-fusion conformation of Langya virus F protein
Components
  • Complex: Vaccine elicted antibody 22F5 bound to post-fusion conformation of Langya virus F protein
    • Complex: Langya virus F protein
    • Complex: 22F5 Fab

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Supramolecule #1: Vaccine elicted antibody 22F5 bound to post-fusion conformation o...

SupramoleculeName: Vaccine elicted antibody 22F5 bound to post-fusion conformation of Langya virus F protein
type: complex / ID: 1 / Parent: 0

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Supramolecule #2: Langya virus F protein

SupramoleculeName: Langya virus F protein / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Langya virus

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Supramolecule #3: 22F5 Fab

SupramoleculeName: 22F5 Fab / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Mus musculus (house mouse)

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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: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 59.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 271130
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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