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- EMDB-48307: Flag-tag Lassa virus spike complex at pH 6.0 -

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Basic information

Entry
Database: EMDB / ID: EMD-48307
TitleFlag-tag Lassa virus spike complex at pH 6.0
Map dataUnfiltered map
Sample
  • Complex: Spike complex of Lassa virus bound by 12.1F and ARN-75039
    • Protein or peptide: Pre-glycoprotein polyprotein GP complex
    • Protein or peptide: Glycoprotein G2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: UNKNOWN LIGAND
  • Ligand: water
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: 2.58 Å
AuthorsKatz M / Cohen-Dvashi H / 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) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48307.png

Downloads & links

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Map

FileDownload / File: emd_48307.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.)
1.04 Å/pix.
x 256 pix.
= 265.728 Å		1.04 Å/pix.
x 256 pix.
= 265.728 Å		1.04 Å/pix.
x 256 pix.
= 265.728 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.038 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.2713358 - 0.65955186
Average (Standard dev.)-0.00015883343 (±0.016632266)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 265.728 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Local-resolution filtered map

Fileemd_48307_additional_1.map
AnnotationLocal-resolution filtered map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_48307_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_48307_half_map_2.map
AnnotationHalf map A
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 bound by 12.1F and ARN-75039

EntireName: Spike complex of Lassa virus bound by 12.1F and ARN-75039
Components
  • Complex: Spike complex of Lassa virus bound by 12.1F and ARN-75039
    • Protein or peptide: Pre-glycoprotein polyprotein GP complex
    • Protein or peptide: Glycoprotein G2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: UNKNOWN LIGAND
  • Ligand: water

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Supramolecule #1: Spike complex of Lassa virus bound by 12.1F and ARN-75039

SupramoleculeName: Spike complex of Lassa virus bound by 12.1F and ARN-75039
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Lassa virus Josiah

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Macromolecule #1: Pre-glycoprotein polyprotein GP complex

MacromoleculeName: Pre-glycoprotein polyprotein GP complex / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Lassa virus Josiah
Molecular weightTheoretical: 22.793809 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TSLYKGVYEL QTLELNMETL NMTMPLSCTK NNSHHYIMVG NETGLELTLT NTSIINHKFC NLSDAHKKNL YDHALMSIIS TFHLSIPNF NQYEAMSCDF NGGKISVQYN LSHSYAGDAA NHCGTVANGV LQTFMRMAWG GSYIALDSGR GNWDCIMTSY Q YLIIQNTT ...String:
TSLYKGVYEL QTLELNMETL NMTMPLSCTK NNSHHYIMVG NETGLELTLT NTSIINHKFC NLSDAHKKNL YDHALMSIIS TFHLSIPNF NQYEAMSCDF NGGKISVQYN LSHSYAGDAA NHCGTVANGV LQTFMRMAWG GSYIALDSGR GNWDCIMTSY Q YLIIQNTT WEDHCQFSRP SPIGYLGLLS QRTRDIYISR RLL

UniProtKB: Pre-glycoprotein polyprotein GP complex

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Macromolecule #2: Glycoprotein G2

MacromoleculeName: Glycoprotein G2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Lassa virus Josiah
Molecular weightTheoretical: 26.828064 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GTFTWTLSDS EGKDTPGGYC LTRWMLIEAE LKCFGNTAVA KCNEKHDEEF CDMLRLFDFN KQAIQRLKAE AQMSIQLINK AVNALINDQ LIMKNHLRDI MGIPYCNYSK YWYLNHTTTG RTSLPKCWLV SNGSYLNETH FSDDIEQQAD NMITEMLQKE Y MERQGKTP ...String:
GTFTWTLSDS EGKDTPGGYC LTRWMLIEAE LKCFGNTAVA KCNEKHDEEF CDMLRLFDFN KQAIQRLKAE AQMSIQLINK AVNALINDQ LIMKNHLRDI MGIPYCNYSK YWYLNHTTTG RTSLPKCWLV SNGSYLNETH FSDDIEQQAD NMITEMLQKE Y MERQGKTP LGLVDLFVFS TSFYLISIFL HLVKIPTHRH IVGKSCPKPH RLNHMGICSC GLYKQPGVPV KWKR

UniProtKB: Pre-glycoprotein polyprotein GP complex

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 15 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #9: UNKNOWN LIGAND

MacromoleculeName: UNKNOWN LIGAND / type: ligand / ID: 9 / Number of copies: 3 / Formula: UNX
Molecular weightTheoretical: 39.098 Da
Chemical component information


ChemComp, No image

ChemComp-UNL:
Unknown ligand

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Macromolecule #10: water

MacromoleculeName: water / type: ligand / ID: 10 / Number of copies: 3 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 6
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: 165000
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 reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.58 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 49874
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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