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- EMDB-53842: LASV tagless in complex with 12.1F Fab reconstructed at C1 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-53842
TitleLASV tagless in complex with 12.1F Fab reconstructed at C1
Map dataMain unfiltered map
Sample
  • Complex: Spike complex of Lassa virus
    • Protein or peptide: LASV 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: 1.99 Å
AuthorsKatz M / Cohen-Dvashi H / Diskin R
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The pH-induced Conformational Changes and Inhibition Mechanism of the Lassa Virus Spike Complex
Authors: Katz M / Diskin R
History
DepositionMay 16, 2025-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: PDBe / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_53842.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain unfiltered map
Voxel sizeX=Y=Z: 0.824 Å
Density
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.09626937 - 0.3268299
Average (Standard dev.)-0.00008066423 (±0.007355982)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 296.64 Å
α=β=γ: 90.0 °

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Supplemental data

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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: LASV 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: LASV spike complex

MacromoleculeName: LASV spike complex / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Lassa virus Josiah
SequenceString: MGQIVTFFQE VPHVIEEVMN IVLIALSVLA VLKGLYNFAT CGLVGLVTFL LLCGRSCTTS LYKGVYELQT LELNMETLNM TMPLSCTKNN SHHYIMVGNE TGLELTLTNT SIINHKFCNL SDAHKKNLYD HALMSIISTF HLSIPNFNQY EAMSCDFNGG KISVQYNLSH ...String:
MGQIVTFFQE VPHVIEEVMN IVLIALSVLA VLKGLYNFAT CGLVGLVTFL LLCGRSCTTS LYKGVYELQT LELNMETLNM TMPLSCTKNN SHHYIMVGNE TGLELTLTNT SIINHKFCNL SDAHKKNLYD HALMSIISTF HLSIPNFNQY EAMSCDFNGG KISVQYNLSH SYAGDAANHC GTVANGVLQT FMRMAWGGSY IALDSGRGNW DCIMTSYQYL IIQNTTWEDH CQFSRPSPIG YLGLLSQRTR DIYISRRLLG TFTWTLSDSE GKDTPGGYCL TRWMLIEAEL KCFGNTAVAK CNEKHDEEFC DMLRLFDFNK QAIQRLKAEA QMSIQLINKA VNALINDQLI MKNHLRDIMG IPYCNYSKYW YLNHTTTGRT SLPKCWLVSN GSYLNETHFS DDIEQQADNM ITEMLQKEYM ERQGKTPLGL VDLFVFSTSF YLISIFLHLV KIPTHRHIVG KSCPKPHRLN HMGICSCGLY KQPGVPVKWK R

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
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
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 1.99 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 448167
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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