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- EMDB-29032: Langya Virus Fusion Protein (LayV-F) in Post-Fusion Conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-29032
TitleLangya Virus Fusion Protein (LayV-F) in Post-Fusion Conformation
Map dataHalf Map B
Sample
  • Complex: Langya Virus Fusion Protein Ectodomain Post-fusion Conformation
    • Protein or peptide: Fusion Protein
KeywordsGlycoprotein / Fusion / Paramyxovirus / Henipavirus / Viral Protein
Biological speciesLangya virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.64 Å
AuthorsMay AJ / Pothula KR / Janowska K / 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: J Virol / Year: 2023
Title: Structures of Langya Virus Fusion Protein Ectodomain in Pre- and Postfusion Conformation.
Authors: Aaron J May / Karunakar Reddy Pothula / Katarzyna Janowska / Priyamvada Acharya /
Abstract: Langya virus (LayV) is a paramyxovirus in the genus, closely related to the deadly Nipah (NiV) and Hendra (HeV) viruses, that was identified in August 2022 through disease surveillance following ...Langya virus (LayV) is a paramyxovirus in the genus, closely related to the deadly Nipah (NiV) and Hendra (HeV) viruses, that was identified in August 2022 through disease surveillance following animal exposure in eastern China. Paramyxoviruses present two glycoproteins on their surface, known as attachment and fusion proteins, that mediate entry into cells and constitute the primary antigenic targets for immune response. Here, we determine cryo-electron microscopy (cryo-EM) structures of the uncleaved LayV fusion protein (F) ectodomain in pre- and postfusion conformations. The LayV-F protein exhibits pre- and postfusion architectures that, despite being highly conserved across paramyxoviruses, show differences in their surface properties, in particular at the apex of the prefusion trimer, that may contribute to antigenic variability. While dramatic conformational changes were visualized between the pre- and postfusion forms of the LayV-F protein, several domains remained invariant, held together by highly conserved disulfides. The LayV-F fusion peptide (FP) is buried within a highly conserved, hydrophobic interprotomer pocket in the prefusion state and is notably less flexible than the rest of the protein, highlighting its "spring-loaded" state and suggesting that the mechanism of pre-to-post transition must involve perturbations to the pocket and release of the fusion peptide. Together, these results offer a structural basis for how the Langya virus fusion protein compares to its Henipavirus relatives and propose a mechanism for the initial step of pre- to postfusion conversion that may apply more broadly to paramyxoviruses. The genus is quickly expanding into new animal hosts and geographic locations. This study compares the structure and antigenicity of the Langya virus fusion protein to other henipaviruses, which have important vaccine and therapeutic development implications. Furthermore, the study proposes a new mechanism to explain the early steps of the fusion initiation process that can be more broadly applied to the family.
History
DepositionDec 6, 2022-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateApr 24, 2024-
Current statusApr 24, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29032.png

Downloads & links

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Map

FileDownload / File: emd_29032.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHalf Map B
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-9.599273999999999 - 10.667344999999999
Average (Standard dev.)0.002202006 (±0.0783378)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 388.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Supplemental map prior to final local refinement.

Fileemd_29032_additional_1.map
AnnotationSupplemental map prior to final local refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Final 3D Refinement

Fileemd_29032_half_map_1.map
AnnotationFinal 3D Refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_29032_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Langya Virus Fusion Protein Ectodomain Post-fusion Conformation

EntireName: Langya Virus Fusion Protein Ectodomain Post-fusion Conformation
Components
  • Complex: Langya Virus Fusion Protein Ectodomain Post-fusion Conformation
    • Protein or peptide: Fusion Protein

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Supramolecule #1: Langya Virus Fusion Protein Ectodomain Post-fusion Conformation

SupramoleculeName: Langya Virus Fusion Protein Ectodomain Post-fusion Conformation
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Langya virus
Molecular weightTheoretical: 180 KDa

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Macromolecule #1: Fusion Protein

MacromoleculeName: Fusion Protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Langya virus
Molecular weightTheoretical: 59.02577 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SLHYDSLSKV GIIKGLTYNY KIKGSPSTKL MVVKLIPNID GVRNCTQKQF DEYKNLVKNV LEPVKLALNA MLDNVKSGNN KYRFAGAIM AGVALGVATA ATVTAGIALH RSNENAQAIA NMKNAIQNTN EAVKQLQLAN KQTLAVIDTI RGEINNNIIP V INQLSCDT ...String:
SLHYDSLSKV GIIKGLTYNY KIKGSPSTKL MVVKLIPNID GVRNCTQKQF DEYKNLVKNV LEPVKLALNA MLDNVKSGNN KYRFAGAIM AGVALGVATA ATVTAGIALH RSNENAQAIA NMKNAIQNTN EAVKQLQLAN KQTLAVIDTI RGEINNNIIP V INQLSCDT IGLSVGIKLT QYYSEILTAF GPALQNPVNT RITIQAISSV FNRNFDELLK IMGYTSGDLY EILHSGLIRG NI IDVDVEA GYIALEIEFP NLTLVPNAVV QELMPISYNV DGDEWVTLVP RFVLTRTTLL SNIDTSRCTV TESSVICDND YAL PMSYEL IGCLQGDTSK CAREKVVSSY VPRFALSDGL VYANCLNTIC RCMDTDTPIS QSLGTTVSLL DNKKCLVYQV GDIL ISVGS YLGEGEYSAD NVELGPPVVI DKIDIGNQLA GINQTLQNAE DYIEKSEEFL KGINPSIGSG YIPEAPRDGQ AYVRK DGEW VLLSTFLGRS LEVLFQGPGH HHHHHHHSAW SHPQFEKGGG SGGGGSGGSA WSHPQFEK

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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
GridModel: Quantifoil R1.2/1.3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6179 / Average electron dose: 56.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 13042103
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.64 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 81802
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: SwissModel / Chain - Initial model type: in silico model
RefinementSpace: REAL
Output model

PDB-8fel:
Langya Virus Fusion Protein (LayV-F) in Post-Fusion Conformation

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