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- EMDB-46965: Immune complex of Lassa virus glycoprotein (Josiah) with polyclon... -

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Entry
Database: EMDB / ID: EMD-46965
TitleImmune complex of Lassa virus glycoprotein (Josiah) with polyclonal Fab from Subject-7 at Day 26
Map dataMain-map
Sample
  • Complex: Immune complex of Lassa virus glycoprotein (Josiah) with polyclonal Fab from Subject-7 at Day 26
    • Complex: Polyclonal Fab from Subject-7 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: Adrian S Enriquez / Ruben Diaz Avalos / Diptiben Parekh / Christopher L Cooper / Gavin Morrow / Thomas W Geisbert / Christopher L Parks / Kathryn M Hastie / Erica Ollmann Saphire /
Abstract: BACKGROUND: Lassa fever, caused by Lassa virus, is a severe disease, endemic in Western Africa, for which no vaccines or therapeutics are yet approved. Understanding the immune responses elicited by ...BACKGROUND: Lassa fever, caused by Lassa virus, is a severe disease, endemic in Western Africa, for which no vaccines or therapeutics are yet approved. Understanding the immune responses elicited by candidate vaccines is key for approval, including characterisation of antibody epitopes recognised and capacity for neutralisation.
METHODS: Here we used negative-stain electron microscopy polyclonal antibody epitope mapping (EMPEM), in-vitro pseudovirus neutralisation assays, and biophysical antibody competition assays to ...METHODS: Here we used negative-stain electron microscopy polyclonal antibody epitope mapping (EMPEM), in-vitro pseudovirus neutralisation assays, and biophysical antibody competition assays to uncover components of polyclonal antibody responses elicited in nonhuman primates 26 days after receipt of a single immunisation with a fully protective, recombinant, replication-competent vesicular stomatitis virus-based vaccine bearing the Lassa virus glycoprotein GPC.
FINDINGS: Although the vaccinee sera are overall poorly-neutralising, we do directly visualise, within the polyclonal pool, antibodies targeting epitopes on GPC that are consistent with ...FINDINGS: Although the vaccinee sera are overall poorly-neutralising, we do directly visualise, within the polyclonal pool, antibodies targeting epitopes on GPC that are consistent with neutralisation, as well as competition with known neutralising mAbs. Nearly every animal, for example, produced antibodies that compete with mAbs against GP1-A and GPC-A neutralising epitopes. The most abundant classes of antibodies, however, are directed against interior interfaces of GPC, while other antibodies recognise post-fusion GPC epitopes not consistent with neutralisation.
INTERPRETATION: It may be that some individual antibodies in the pool are neutralising, but that the abundance of non-neutralising epitopes reduces potency as measured at the polyclonal level. The ...INTERPRETATION: It may be that some individual antibodies in the pool are neutralising, but that the abundance of non-neutralising epitopes reduces potency as measured at the polyclonal level. The finding, however, neutralisation-consistent sites and competition with known neutralising antibodies are important steps in vaccine design toward eliciting more potent neutralisation.
FUNDING: A complete list of funding bodies that supported this study is presented in the Funding section.
History
DepositionSep 9, 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_46965.png

Downloads & links

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Map

FileDownload / File: emd_46965.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: 0.6
Minimum - Maximum-2.6959672 - 8.336733000000001
Average (Standard dev.)-0.0019481265 (±0.15134014)
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_46965_half_map_1.map
AnnotationHalf-map A
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: Half-map B

Fileemd_46965_half_map_2.map
AnnotationHalf-map B
Projections & Slices
AxesZYX

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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-7 at Day 26
Components
  • Complex: Immune complex of Lassa virus glycoprotein (Josiah) with polyclonal Fab from Subject-7 at Day 26
    • Complex: Polyclonal Fab from Subject-7 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-7 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-7 at Day 26

SupramoleculeName: Polyclonal Fab from Subject-7 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: 13091
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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