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- EMDB-48303: Native tagless Lassa virus spike complex pH 6.0 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-48303
TitleNative tagless Lassa virus spike complex pH 6.0
Map dataUnfiltered map
Sample
  • Complex: Spike complex of Lassa virus bound by 12.1F and ARN-75039
    • Protein or peptide: Glycoprotein G2
    • Protein or peptide: Glycoprotein G1
    • Protein or peptide: 12.1F Heavy chain
    • Protein or peptide: 12.1F Light chain
  • 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 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.02 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: Cohen-Dvashi H / Katz M / Diskin R
History
DepositionDec 13, 2024-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: RCSB / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_48303.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnfiltered map
Voxel sizeX=Y=Z: 0.8242 Å
Density
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.30673525 - 0.82287616
Average (Standard dev.)-0.0004860686 (±0.019186197)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 296.712 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 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: Glycoprotein G2
    • Protein or peptide: Glycoprotein G1
    • Protein or peptide: 12.1F Heavy chain
    • Protein or peptide: 12.1F Light chain
  • 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-#4
Source (natural)Organism: Lassa virus Josiah

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Macromolecule #1: Glycoprotein G2

MacromoleculeName: Glycoprotein G2 / type: protein_or_peptide / ID: 1 / 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 #2: Glycoprotein G1

MacromoleculeName: Glycoprotein G1 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Lassa virus Josiah
Molecular weightTheoretical: 29.064402 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGQIVTFFQE VPHVIEEVMN IVLIALSVLA VLKGLYNFAT CGLVGLVTFL LLCGRSCTTS LYKGVYELQT LELNMETLNM TMPLSCTKN NSHHYIMVGN ETGLELTLTN TSIINHKFCN LSDAHKKNLY DHALMSIIST FHLSIPNFNQ YEAMSCDFNG G KISVQYNL ...String:
MGQIVTFFQE VPHVIEEVMN IVLIALSVLA VLKGLYNFAT CGLVGLVTFL LLCGRSCTTS LYKGVYELQT LELNMETLNM TMPLSCTKN NSHHYIMVGN ETGLELTLTN TSIINHKFCN LSDAHKKNLY DHALMSIIST FHLSIPNFNQ YEAMSCDFNG G KISVQYNL SHSYAGDAAN HCGTVANGVL QTFMRMAWGG SYIALDSGRG NWDCIMTSYQ YLIIQNTTWE DHCQFSRPSP IG YLGLLSQ RTRDIYISRR LL

UniProtKB: Pre-glycoprotein polyprotein GP complex

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Macromolecule #3: 12.1F Heavy chain

MacromoleculeName: 12.1F Heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.79373 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQESGAG LLKPSETLSL SCTVDGESFN GFFWTWIRQP PGKGLEWIGE INHLASTGYN PSLKSRVTIS VDTSKNQFSL KLTSVTAAD TAVYYCARGY SYGFAWPNYH YLDVWGKGTT VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ...String:
QVQLQESGAG LLKPSETLSL SCTVDGESFN GFFWTWIRQP PGKGLEWIGE INHLASTGYN PSLKSRVTIS VDTSKNQFSL KLTSVTAAD TAVYYCARGY SYGFAWPNYH YLDVWGKGTT VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DKRVEPKSCD KTHGGDYKDD DD KGTENLY FQ

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Macromolecule #4: 12.1F Light chain

MacromoleculeName: 12.1F Light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.492086 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPAT LSLSPGERAT LSCRASQSVS SYLAWYQHKP GQAPRLLIYG ASKRATGIPS RFSGSGSGTD FSLTISSLEP EDFAVYYCQ HRSDWRTTFG QGTRLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
EIVLTQSPAT LSLSPGERAT LSCRASQSVS SYLAWYQHKP GQAPRLLIYG ASKRATGIPS RFSGSGSGTD FSLTISSLEP EDFAVYYCQ HRSDWRTTFG QGTRLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #13: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 13 / Number of copies: 12 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #14: UNKNOWN LIGAND

MacromoleculeName: UNKNOWN LIGAND / type: ligand / ID: 14 / Number of copies: 3 / Formula: UNX
Molecular weightTheoretical: 54.938 Da
Chemical component information


ChemComp, No image

ChemComp-UNL:
Unknown ligand

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Macromolecule #15: water

MacromoleculeName: water / type: ligand / ID: 15 / Number of copies: 1453 / 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: 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: 2.02 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 945950
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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