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- EMDB-46863: Immune complex of Lassa virus glycoprotein (Josiah) with polyclon... -

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Basic information

Entry
Database: EMDB / ID: EMD-46863
TitleImmune complex of Lassa virus glycoprotein (Josiah) with polyclonal Fab from Subject-9 at Day 26
Map dataMain-map
Sample
  • Complex: Immune complex of Lassa virus glycoprotein (Josiah) with polyclonal Fab from Subject-9 at Day 26
    • Complex: Polyclonal Fab from Subject-9 at Day 26
      • Complex: Lassa virus glycoprotein (Josiah)
KeywordsViral glycoprotein / Lassa virus (Josiah) / VIRAL PROTEIN / Immune complex / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesLassa virus Josiah / Macaca fascicularis (crab-eating macaque)
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsEnriquez AS / Saphire EO
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 A1132244 United States
Other privateA08154
CitationJournal: Ebiomedicine / Year: 2025
Title: Mapping the antibody response to Lassa virus vaccination of non-human primates.
Authors: Enriquez AS / Avalos RD / Parekh D / Cooper CL / Morrow G / Geisbert TW / Parks CL / Hastie KM / Saphire EO
History
DepositionSep 3, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46863.png

Downloads & links

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Map

FileDownload / File: emd_46863.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain-map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.8 Å/pix.
x 64 pix.
= 435.2 Å		6.8 Å/pix.
x 64 pix.
= 435.2 Å		6.8 Å/pix.
x 64 pix.
= 435.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-1.4010911 - 7.6620264
Average (Standard dev.)-0.0052837334 (±0.13098928)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 435.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-map A

Fileemd_46863_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_46863_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 : Immune complex of Lassa virus glycoprotein (Josiah) with polyclon...

EntireName: Immune complex of Lassa virus glycoprotein (Josiah) with polyclonal Fab from Subject-9 at Day 26
Components
  • Complex: Immune complex of Lassa virus glycoprotein (Josiah) with polyclonal Fab from Subject-9 at Day 26
    • Complex: Polyclonal Fab from Subject-9 at Day 26
      • Complex: Lassa virus glycoprotein (Josiah)

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Supramolecule #1: Immune complex of Lassa virus glycoprotein (Josiah) with polyclon...

SupramoleculeName: Immune complex of Lassa virus glycoprotein (Josiah) with polyclonal Fab from Subject-9 at Day 26
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Lassa virus Josiah

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Supramolecule #2: Polyclonal Fab from Subject-9 at Day 26

SupramoleculeName: Polyclonal Fab from Subject-9 at Day 26 / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Macaca fascicularis (crab-eating macaque)

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Supramolecule #3: Lassa virus glycoprotein (Josiah)

SupramoleculeName: Lassa virus glycoprotein (Josiah) / type: complex / ID: 3 / Parent: 2
Source (natural)Organism: Lassa virus Josiah

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.01 mg/mL
BufferpH: 7.5 / Details: 50mM Tris pH 7.5, 150mM NaCl
StainingType: NEGATIVE / Material: Uranyl Acetate
GridModel: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.3.0) / Number images used: 1135
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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