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- EMDB-41642: Langya henipavirus postfusion F protein in complex with 4G5 Fab, ... -

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Basic information

Entry
Database: EMDB / ID: EMD-41642
TitleLangya henipavirus postfusion F protein in complex with 4G5 Fab, local refinement of the viral membrane proximal region
Map data
Sample
  • Complex: Langya henipavirus postfusion fusion protein in complex with 4G5 Fab
    • Protein or peptide: Fusion glycoprotein
    • Protein or peptide: 4G5 light chain
    • Protein or peptide: 4G5 heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsLangya / henipavirus / fusion protein / postfusion / LayVF / SSGCID / VIRAL PROTEIN-IMMUNE SYSTEM complex / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyFusion glycoprotein
Function and homology information
Biological speciesLangya virus / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 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-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41642.png

Downloads & links

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Map

FileDownload / File: emd_41642.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-2.097761 - 3.3979666
Average (Standard dev.)0.0005583896 (±0.03630853)
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_41642_additional_1.map
AnnotationUnsharpened
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Half map: #2

Fileemd_41642_half_map_1.map
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Half map: #1

Fileemd_41642_half_map_2.map
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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: Fusion glycoprotein
    • Protein or peptide: 4G5 light chain
    • Protein or peptide: 4G5 heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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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: #3, #1-#2
Source (natural)Organism: Langya virus

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Macromolecule #1: 4G5 light chain

MacromoleculeName: 4G5 light chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.655939 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString:
DIQMTQSPAS LSASVGETVT ITCRASGNIH NYLAWYQQKQ GKSPQLLVYS AKTLADGVPS RFSGSGSGTQ YSLKINSLQP EDFGSYYCQ HFWSSPRTFG GGTKLEIK

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Macromolecule #2: 4G5 heavy chain

MacromoleculeName: 4G5 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.108406 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString:
EVQLQQSGAD LVKPGASVKL SCTASGFNIK DTYIHWVKQR PEQGLEWIGR IDPANDNFKY DPKFQGKATI TTDTSSNTAY LQLSSLTSE DTAVYYCASV ITTTGYALDY WGQGTSVTVS S

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Macromolecule #3: Fusion glycoprotein

MacromoleculeName: Fusion glycoprotein / type: protein_or_peptide / ID: 3 / 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

UniProtKB: Fusion glycoprotein

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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
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: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 60440

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