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- EMDB-17428: The spike complex of the Lujo Virus -

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Basic information

Entry
Database: EMDB / ID: EMD-17428
TitleThe spike complex of the Lujo Virus
Map dataUnfiltered map
Sample
  • Complex: Spike complex from the Lujo virus
    • Protein or peptide: Glycoprotein
    • Protein or peptide: Glycoprotein
    • Protein or peptide: Glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: SODIUM ION
KeywordsSpike complex / VIRAL PROTEIN
Function / homologyArenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein / host cell Golgi apparatus / viral envelope / membrane / Glycoprotein
Function and homology information
Biological speciesLujo mammarenavirus / Mammarenavirus lujoense
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsEilon-Ashkenazy M / Diskin R
Funding support Israel, 1 items
OrganizationGrant numberCountry
Israel Science Foundation209/20 Israel
CitationJournal: To Be Published
Title: The spike complex of the Lujo Virus
Authors: Eilon-Ashkenazy M / Diskin R
History
DepositionMay 23, 2023-
Header (metadata) releaseJun 12, 2024-
Map releaseJun 12, 2024-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17428.png

Downloads & links

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Map

FileDownload / File: emd_17428.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnfiltered map
Voxel sizeX=Y=Z: 0.824 Å
Density
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.24959014 - 0.47432563
Average (Standard dev.)0.0006893183 (±0.016787007)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 210.944 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17428_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unfiltered map

Fileemd_17428_additional_1.map
AnnotationUnfiltered map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered map

Fileemd_17428_half_map_1.map
AnnotationUnfiltered map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered map

Fileemd_17428_half_map_2.map
AnnotationUnfiltered map
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 from the Lujo virus

EntireName: Spike complex from the Lujo virus
Components
  • Complex: Spike complex from the Lujo virus
    • Protein or peptide: Glycoprotein
    • Protein or peptide: Glycoprotein
    • Protein or peptide: Glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: SODIUM ION

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Supramolecule #1: Spike complex from the Lujo virus

SupramoleculeName: Spike complex from the Lujo virus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Lujo mammarenavirus

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Macromolecule #1: Glycoprotein

MacromoleculeName: Glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mammarenavirus lujoense
Molecular weightTheoretical: 19.017572 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SSLLSGFNLE TVHFNMSLLS SIPMVSEQQH CIQHNHSSIT FSLLTNKSDL EKCNFTRLQA VDRVIFDLFR EFHHRVGDFP VTSDLKCSH NTSYRVIEYE VTKESLPRLQ EAVSTLFPDL HLSEDRFLQI QAHDDKNCTG LHPLNYLRLL KENSETHYKV R KLM

UniProtKB: Glycoprotein

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Macromolecule #2: Glycoprotein

MacromoleculeName: Glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mammarenavirus lujoense
Molecular weightTheoretical: 28.267627 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: KLFQWSLSDE TGSPLPGGHC LERWLIFASD IKCFDNAAIA KCNKEHDEEF CDMLRLFDYN KASIAKLRGE ASSSINLLSG RINAIISDT LLMRSSLKRL MGIPYCNYTK FWYLNHTKLG IHSLPRCWLV SNGSYLNETK FTHDMEDEAD KLLTEMLKKE Y VRRQEKTP ...String:
KLFQWSLSDE TGSPLPGGHC LERWLIFASD IKCFDNAAIA KCNKEHDEEF CDMLRLFDYN KASIAKLRGE ASSSINLLSG RINAIISDT LLMRSSLKRL MGIPYCNYTK FWYLNHTKLG IHSLPRCWLV SNGSYLNETK FTHDMEDEAD KLLTEMLKKE Y VRRQEKTP ITLMDILMFS VSFYMFSVTL CICNIPTHRH ITGLPCPKPH RLRKNGTCAC GFFKSINRST GWAKHGGDYK DD DDKGSGT

UniProtKB: Glycoprotein

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Macromolecule #3: Glycoprotein

MacromoleculeName: Glycoprotein / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mammarenavirus lujoense
Molecular weightTheoretical: 6.501998 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MGQIVAVFQA IPEILNEAIN IVIIVIIMFT LIKGVFNLYK SGLFQLVIFL LLCGKRCD

UniProtKB: Glycoprotein

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 21 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #8: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 8 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 41.0 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: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 87868
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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