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- EMDB-48308: Map of LASV spike complex after exposure to pH 5.0 and re-equilib... -

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Basic information

Entry
Database: EMDB / ID: EMD-48308
TitleMap of LASV spike complex after exposure to pH 5.0 and re-equilibration to pH 8.0
Map dataUnfiltered map
Sample
  • Complex: Spike complex of Lassa virus
    • Protein or peptide: Lassa virus spike complex
KeywordsSpike complex / VIRAL PROTEIN
Function / homology
Function and homology information


host cell Golgi membrane / receptor-mediated endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / metal ion binding / membrane
Similarity search - Function
Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein
Similarity search - Domain/homology
Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesLassa virus Josiah
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKatz M / Diskin R
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Host Microbe / Year: 2025
Title: pH-induced conformational changes and inhibition of the Lassa virus spike complex.
Authors: Michael Katz / Hadas Cohen-Dvashi / Sarah Borni / John Ruedas / Greg Henkel / Ken McCormack / Ron Diskin /
Abstract: Lassa virus (LASV) is a devastating human pathogen with no vaccines and limited therapeutics. The LASV class-I spike complex engages target cells via binding its primary host receptor, matriglycan, ...Lassa virus (LASV) is a devastating human pathogen with no vaccines and limited therapeutics. The LASV class-I spike complex engages target cells via binding its primary host receptor, matriglycan, followed by macropinocytosis and binding of its secondary receptor, lysosomal-associated membrane protein 1 (LAMP1), to trigger virus fusion. This process occurs across multiple pH-dependent steps, but the molecular events remain largely unknown. Through high-resolution structures, we study the pH-induced conformational changes of the spike preceding membrane fusion. We reveal pH-sensitive metal coordination sites that control the integrity of the spike's native state, elucidate a reorganization of the spike's transmembrane region, and provide a mechanism for dissociation from its primary receptor. Using the entry inhibitor ARN-75039, we validate our findings and establish the molecular basis for the binding and function of this investigational drug. These data define the molecular basis for the cell entry of LASV and will promote efforts in combating this virus and potentially related viral pathogens.
History
DepositionDec 13, 2024-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48308.png

Downloads & links

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Map

FileDownload / File: emd_48308.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnfiltered map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 256 pix.
= 210.995 Å		0.82 Å/pix.
x 256 pix.
= 210.995 Å		0.82 Å/pix.
x 256 pix.
= 210.995 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8242 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.15254116 - 0.2914739
Average (Standard dev.)0.0004609289 (±0.012503131)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 210.9952 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: DeepEMhanced map

Fileemd_48308_additional_1.map
AnnotationDeepEMhanced map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_48308_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_48308_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Spike complex of Lassa virus

EntireName: Spike complex of Lassa virus
Components
  • Complex: Spike complex of Lassa virus
    • Protein or peptide: Lassa virus spike complex

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Supramolecule #1: Spike complex of Lassa virus

SupramoleculeName: Spike complex of Lassa virus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Lassa virus Josiah

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Macromolecule #1: Lassa virus spike complex

MacromoleculeName: Lassa virus spike complex / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: MGQIVTFFQE VPHVIEEVMN IVLIALSVLA VLKGLYNFAT CGLVGLVTFL LLCGRSCTTS LYKGVYELQ TLELNMETLN MTMPLSCTKN NSHHYIMVGN ETGLELTLTN TSIINHKFCN L SDAHKKNL YDHALMSIIS TFHLSIPNFN QYEAMSCDFN GGKISVQYNL ...String:
MGQIVTFFQE VPHVIEEVMN IVLIALSVLA VLKGLYNFAT CGLVGLVTFL LLCGRSCTTS LYKGVYELQ TLELNMETLN MTMPLSCTKN NSHHYIMVGN ETGLELTLTN TSIINHKFCN L SDAHKKNL YDHALMSIIS TFHLSIPNFN QYEAMSCDFN GGKISVQYNL SHSYAGDAAN HC GTVANGV LQTFMRMAWG GSYIALDSGR GNWDCIMTSY QYLIIQNTTW EDHCQFSRPS PIG YLGLLS QRTRDIYISR RLLGTFTWTL SDSEGKDTPG GYCLTRWMLI EAELKCFGNT AVAK CNEKH DEEFCDMLRL FDFNKQAIQR LKAEAQMSIQ LINKAVNALI NDQLIMKNHL RDIMG IPYC NYSKYWYLNH TTTGRTSLPK CWLVSNGSYL NETHFSDDIE QQADNMITEM LQKEYM ERQ GKTPLGLVDL FVFSTSFYLI SIFLHLVKIP THRHIVGKSC PKPHRLNHMG ICSCGLY KQ PGVPVKWKRG GGSDYKDDDD K

UniProtKB: Pre-glycoprotein polyprotein GP complex

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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

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 38.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: stochastic gradient descent
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 62155
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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