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- EMDB-28187: Cryo-EM I1 reconstruction of antibody SKV09 in complex with VEEV ... -

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Basic information

Entry
Database: EMDB / ID: EMD-28187
TitleCryo-EM I1 reconstruction of antibody SKV09 in complex with VEEV alphavirus VLP
Map dataVLP I1 map
Sample
  • Complex: Cryo-EM I1 reconstruction of antibody SKV09 in complex with VEEV alphavirus VLP
Keywordsantibody / alphavirus / VEEV / spike / glycoprotein / VIRAL PROTEIN
Biological speciesVenezuelan equine encephalitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 7.0 Å
AuthorsCasner RG / Verardi R / Roederer M / Shapiro L
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Cell / Year: 2023
Title: Vaccine elicitation and structural basis for antibody protection against alphaviruses.
Authors: Matthew S Sutton / Sergei Pletnev / Victoria Callahan / Sungyoul Ko / Yaroslav Tsybovsky / Tatsiana Bylund / Ryan G Casner / Gabriele Cerutti / Christina L Gardner / Veronica Guirguis / ...Authors: Matthew S Sutton / Sergei Pletnev / Victoria Callahan / Sungyoul Ko / Yaroslav Tsybovsky / Tatsiana Bylund / Ryan G Casner / Gabriele Cerutti / Christina L Gardner / Veronica Guirguis / Raffaello Verardi / Baoshan Zhang / David Ambrozak / Margaret Beddall / Hong Lei / Eun Sung Yang / Tracy Liu / Amy R Henry / Reda Rawi / Arne Schön / Chaim A Schramm / Chen-Hsiang Shen / Wei Shi / Tyler Stephens / Yongping Yang / Maria Burgos Florez / Julie E Ledgerwood / Crystal W Burke / Lawrence Shapiro / Julie M Fox / Peter D Kwong / Mario Roederer /
Abstract: Alphaviruses are RNA viruses that represent emerging public health threats. To identify protective antibodies, we immunized macaques with a mixture of western, eastern, and Venezuelan equine ...Alphaviruses are RNA viruses that represent emerging public health threats. To identify protective antibodies, we immunized macaques with a mixture of western, eastern, and Venezuelan equine encephalitis virus-like particles (VLPs), a regimen that protects against aerosol challenge with all three viruses. Single- and triple-virus-specific antibodies were isolated, and we identified 21 unique binding groups. Cryo-EM structures revealed that broad VLP binding inversely correlated with sequence and conformational variability. One triple-specific antibody, SKT05, bound proximal to the fusion peptide and neutralized all three Env-pseudotyped encephalitic alphaviruses by using different symmetry elements for recognition across VLPs. Neutralization in other assays (e.g., chimeric Sindbis virus) yielded variable results. SKT05 bound backbone atoms of sequence-diverse residues, enabling broad recognition despite sequence variability; accordingly, SKT05 protected mice against Venezuelan equine encephalitis virus, chikungunya virus, and Ross River virus challenges. Thus, a single vaccine-elicited antibody can protect in vivo against a broad range of alphaviruses.
History
DepositionSep 17, 2022-
Header (metadata) releaseJul 26, 2023-
Map releaseJul 26, 2023-
UpdateJul 26, 2023-
Current statusJul 26, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28187.png

Downloads & links

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Map

FileDownload / File: emd_28187.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVLP I1 map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.32 Å/pix.
x 450 pix.
= 1494. Å		3.32 Å/pix.
x 450 pix.
= 1494. Å		3.32 Å/pix.
x 450 pix.
= 1494. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 950.0
Minimum - Maximum-586.261200000000031 - 2526.76339999999982
Average (Standard dev.)1.1360728 (±251.873979999999989)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 1494.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: VLP I1 half map 1

Fileemd_28187_half_map_1.map
AnnotationVLP I1 half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: VLP I1 half map 2

Fileemd_28187_half_map_2.map
AnnotationVLP I1 half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM I1 reconstruction of antibody SKV09 in complex with VEEV ...

EntireName: Cryo-EM I1 reconstruction of antibody SKV09 in complex with VEEV alphavirus VLP
Components
  • Complex: Cryo-EM I1 reconstruction of antibody SKV09 in complex with VEEV alphavirus VLP

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Supramolecule #1: Cryo-EM I1 reconstruction of antibody SKV09 in complex with VEEV ...

SupramoleculeName: Cryo-EM I1 reconstruction of antibody SKV09 in complex with VEEV alphavirus VLP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Venezuelan equine encephalitis virus

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 53462
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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