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- EMDB-43593: Langya Virus attachment (G) glycoprotein with K85L/L86K mutation -

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Basic information

Entry
Database: EMDB / ID: EMD-43593
TitleLangya Virus attachment (G) glycoprotein with K85L/L86K mutation
Map data
Sample
  • Complex: Langya virus attachment (G) protein
    • Protein or peptide: Langya virus attachment (G) protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordslangya / attachment / glycoprotein / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / VIRAL PROTEIN
Biological speciesLangya virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsGibson CG / McCallum MM / Veesler DV
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) 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
DepositionFeb 2, 2024-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43593.png

Downloads & links

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Map

FileDownload / File: emd_43593.map.gz / Format: CCP4 / Size: 325 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.)
0.89 Å/pix.
x 440 pix.
= 391.6 Å		0.89 Å/pix.
x 440 pix.
= 391.6 Å		0.89 Å/pix.
x 440 pix.
= 391.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.89 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.265
Minimum - Maximum-1.3141979 - 2.0423117
Average (Standard dev.)0.0008253337 (±0.035538234)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 391.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_43593_additional_1.map
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Half map: #1

Fileemd_43593_half_map_1.map
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Half map: #2

Fileemd_43593_half_map_2.map
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Sample components

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Entire : Langya virus attachment (G) protein

EntireName: Langya virus attachment (G) protein
Components
  • Complex: Langya virus attachment (G) protein
    • Protein or peptide: Langya virus attachment (G) protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Langya virus attachment (G) protein

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

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Macromolecule #1: Langya virus attachment (G) protein

MacromoleculeName: Langya virus attachment (G) protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Langya virus
Molecular weightTheoretical: 59.402613 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LKAIQAMLKI IQDEVNSLKE MLVSLDQLVK TEIKPKVSLI NTAVSVSIPA QISNLQTKVL QKLVYLEESI TKQCT(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) ...String:
LKAIQAMLKI IQDEVNSLKE MLVSLDQLVK TEIKPKVSLI NTAVSVSIPA QISNLQTKVL QKLVYLEESI TKQCT(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) DTTDDDKVDT TIKPVEYYKP DGCNKTNDHF TMQPGVNFYT VPNLGPSSSS ADECYTNPS FSIGSSIYMF SQEIRKTDCT TGEILSIQIV LGRIVDKGQQ GPQASPLLVW SVPNPKIINS CAVAAGDETG W VLCSVTLT AASGEPIPHM FDGFWLYKFE PDTEVVAYRI TGFAYLLDKV YDSVFIGKGG GIQRGNDLYF QMFGLSRNRQ SI KALCEHG SCL(UNK)(UNK)(UNK)(UNK)GGY QVLCDRAVMS FGSEESLISN AYLKVNDVAS GKPTIISQTF PPSDSYK GS NGRIYTIGER YGIYLAPSSW NRYLRFGLTP DISVRSTTWL KEKDPIMKVL TTCTNTDKDM CPEICNTRGY QDIFPLSE D SSFYTYIGIT PSNEGTKSFV AVKDDAGHVA SITILPNYYS ITSATISCFM YKEEIWCIAV TEGRKQKENP QRIYAHSYR VQKMCFNI

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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: 4 / 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: 7.8
GridModel: UltrAuFoil / Material: GOLD
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 47.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm

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Image processing

Startup modelType of model: OTHER / Details: CryoSPARC ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 79301
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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