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- EMDB-41641: Langya henipavirus postfusion F protein in complex with the 4G5 F... -

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Basic information

Entry
Database: EMDB / ID: EMD-41641
TitleLangya henipavirus postfusion F protein in complex with the 4G5 Fab, local refinement of the viral membrane distal region
Map data
Sample
  • Complex: Langya henipavirus postfusion F protein
    • Protein or peptide: Langya henipavirus postfusion F protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsLangya / henipavirus / fusion protein / postfusion / LayVF / SSGCID / VIRAL PROTEIN / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Biological speciesLangya virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsWang Z / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / 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-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41641.png

Downloads & links

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Map

FileDownload / File: emd_41641.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.98 Å/pix.
x 480 pix.
= 472.08 Å		0.98 Å/pix.
x 480 pix.
= 472.08 Å		0.98 Å/pix.
x 480 pix.
= 472.08 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9835 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-1.6782268 - 2.9894524
Average (Standard dev.)0.0005544074 (±0.038732972)
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_41641_additional_1.map
AnnotationUnsharpened
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Half map: #2

Fileemd_41641_half_map_1.map
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Half map: #1

Fileemd_41641_half_map_2.map
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Sample components

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Entire : Langya henipavirus postfusion F protein

EntireName: Langya henipavirus postfusion F protein
Components
  • Complex: Langya henipavirus postfusion F protein
    • Protein or peptide: Langya henipavirus postfusion F protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Langya henipavirus postfusion F protein

SupramoleculeName: Langya henipavirus postfusion F protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Langya virus

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Macromolecule #1: Langya henipavirus postfusion F protein

MacromoleculeName: Langya henipavirus postfusion F protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Langya virus
Molecular weightTheoretical: 58.480812 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAFLKSAIIC YLLFYPHIVK SSLHYDSLSK VGIIKGLTYN YKIKGSPSTK LMVVKLIPNI DGVRNCTQKQ FDEYKNLVKN VLEPVKLAL NAMLDNVKSG NNKYRFAGAI MAGVALGVAT AATVTAGIAL HRSNENAQAI ANMKNAIQNT NEAVKQLQLA N KQTLAVID ...String:
MAFLKSAIIC YLLFYPHIVK SSLHYDSLSK VGIIKGLTYN YKIKGSPSTK LMVVKLIPNI DGVRNCTQKQ FDEYKNLVKN VLEPVKLAL NAMLDNVKSG NNKYRFAGAI MAGVALGVAT AATVTAGIAL HRSNENAQAI ANMKNAIQNT NEAVKQLQLA N KQTLAVID TIRGEINNNI IPVINQLSCD TIGLSVGIKL TQYYSEILTA FGPALQNPVN TRITIQAISS VFNRNFDELL KI MGYTSGD LYEILHSGLI RGNIIDVDVE AGYIALEIEF PNLTLVPNAV VQELMPISYN VDGDEWVTLV PRFVLTRTTL LSN IDTSRC TVTESSVICD NDYALPMSYE LIGCLQGDTS KCAREKVVSS YVPRFALSDG LVYANCLNTI CRCMDTDTPI SQSL GTTVS LLDNKKCLVY QVGDILISVG SYLGEGEYSA DNVELGPPVV IDKIDIGNQL AGINQTLQNA EDYIEKSEEF LKGIN PSMK QIEDKIEEIL SKIYHIENEI ARIKKLIGEA PGGSIEGRGS GGGSHHHHHH

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / 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: 8
GridModel: Quantifoil R2/2 / Material: GOLD / Details: 10mM OG
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 24 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

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

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 60440
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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