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- EMDB-41644: Langya henipavirus postfusion fusion protein in complex with 4G5 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-41644
TitleLangya henipavirus postfusion fusion protein in complex with 4G5 Fab (global refinement)
Map data
Sample
  • Complex: Langya henipavirus postfusion fusion protein in complex with 4G5 Fab
    • Protein or peptide: Langya henipavirus fusion protein in postfusion state
    • Protein or peptide: 4G5 Fab heavy chain variable domain
    • Protein or peptide: 4G5 Fab light chain variable domain
KeywordsLangya / henipavirus / fusion protein / postfusion / LayVF / SSGCID / VIRAL PROTEIN
Biological speciesLangya virus / Mus sp. (mice)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsWang Z / Veesler D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI158186 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Structure and design of Langya virus glycoprotein antigens.
Authors: Zhaoqian Wang / Matthew McCallum / Lianying Yan / Cecily A Gibson / William Sharkey / Young-Jun Park / Ha V Dang / Moushimi Amaya / Ashley Person / Christopher C Broder / David Veesler /
Abstract: Langya virus (LayV) is a recently discovered henipavirus (HNV), isolated from febrile patients in China. HNV entry into host cells is mediated by the attachment (G) and fusion (F) glycoproteins which ...Langya virus (LayV) is a recently discovered henipavirus (HNV), isolated from febrile patients in China. HNV entry into host cells is mediated by the attachment (G) and fusion (F) glycoproteins which are the main targets of neutralizing antibodies. We show here that the LayV F and G glycoproteins promote membrane fusion with human, mouse, and hamster target cells using a different, yet unknown, receptor than Nipah virus (NiV) and Hendra virus (HeV) and that NiV- and HeV-elicited monoclonal and polyclonal antibodies do not cross-react with LayV F and G. We determined cryoelectron microscopy structures of LayV F, in the prefusion and postfusion states, and of LayV G, revealing their conformational landscape and distinct antigenicity relative to NiV and HeV. We computationally designed stabilized LayV G constructs and demonstrate the generalizability of an HNV F prefusion-stabilization strategy. Our data will support the development of vaccines and therapeutics against LayV and closely related HNVs.
History
DepositionAug 18, 2023-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41644.png

Downloads & links

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Map

FileDownload / File: emd_41644.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.9835 Å
Density
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.9868132 - 2.8311188
Average (Standard dev.)0.0005579848 (±0.03304321)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 472.08002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened

Fileemd_41644_additional_1.map
AnnotationUnsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_41644_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_41644_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Sample components

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Entire : Langya henipavirus postfusion fusion protein in complex with 4G5 Fab

EntireName: Langya henipavirus postfusion fusion protein in complex with 4G5 Fab
Components
  • Complex: Langya henipavirus postfusion fusion protein in complex with 4G5 Fab
    • Protein or peptide: Langya henipavirus fusion protein in postfusion state
    • Protein or peptide: 4G5 Fab heavy chain variable domain
    • Protein or peptide: 4G5 Fab light chain variable domain

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Supramolecule #1: Langya henipavirus postfusion fusion protein in complex with 4G5 Fab

SupramoleculeName: Langya henipavirus postfusion fusion protein in complex with 4G5 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Langya virus

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Macromolecule #1: Langya henipavirus fusion protein in postfusion state

MacromoleculeName: Langya henipavirus fusion protein in postfusion state / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Langya virus
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAFLKSAIIC YLLFYPHIVK SSLHYDSLSK VGIIKGLTYN YKIKGSPSTK LMVVKLIPNI DGVRNCTQKQ FDEYKNLVKN VLEPVKLALN AMLDNVKSGN NKYRFAGAIM AGVALGVATA ATVTAGIALH RSNENAQAIA NMKNAIQNTN EAVKQLQLAN KQTLAVIDTI ...String:
MAFLKSAIIC YLLFYPHIVK SSLHYDSLSK VGIIKGLTYN YKIKGSPSTK LMVVKLIPNI DGVRNCTQKQ FDEYKNLVKN VLEPVKLALN AMLDNVKSGN NKYRFAGAIM AGVALGVATA ATVTAGIALH RSNENAQAIA NMKNAIQNTN EAVKQLQLAN KQTLAVIDTI RGEINNNIIP VINQLSCDTI GLSVGIKLTQ YYSEILTAFG PALQNPVNTR ITIQAISSVF NRNFDELLKI MGYTSGDLYE ILHSGLIRGN IIDVDVEAGY IALEIEFPNL TLVPNAVVQE LMPISYNVDG DEWVTLVPRF VLTRTTLLSN IDTSRCTVTE SSVICDNDYA LPMSYELIGC LQGDTSKCAR EKVVSSYVPR FALSDGLVYA NCLNTICRCM DTDTPISQSL GTTVSLLDNK KCLVYQVGDI LISVGSYLGE GEYSADNVEL GPPVVIDKID IGNQLAGINQ TLQNAEDYIE KSEEFLKGIN PSMKQIEDKI EEILSKIYHI ENEIARIKKL IGEAPGGSIE GRGSGGGSHH HHHH

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Macromolecule #2: 4G5 Fab heavy chain variable domain

MacromoleculeName: 4G5 Fab heavy chain variable domain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus sp. (mice)
SequenceString:
EVQLQQSGAD LVKPGASVKL SCTASGFNIK DTYIHWVKQR PEQGLEWIGR IDPANDNFKY DPKFQGKATI TTDTSSNTAY LQLSSLTSED TAVYYCASVI TTTGYALDYW GQGTSVTVSS

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Macromolecule #3: 4G5 Fab light chain variable domain

MacromoleculeName: 4G5 Fab light chain variable domain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus sp. (mice)
SequenceString:
DIQMTQSPAS LSASVGETVT ITCRASGNIH NYLAWYQQKQ GKSPQLLVYS AKTLADGVPS RFSGSGSGTQ YSLKINSLQP EDFGSYYCQH FWSSPRTFGG GTKLEIK

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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 / Chamber humidity: 100 % / Chamber temperature: 24 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.7 µm / Nominal defocus min: 1.3 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 63.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 60440

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