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- EMDB-28117: Eastern Equine Encephalitis Virus-Like Particle in Complex with S... -

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Basic information

Entry
Database: EMDB / ID: EMD-28117
TitleEastern Equine Encephalitis Virus-Like Particle in Complex with SKE26 Fab
Map data
Sample
  • Complex: Eastern Equine Encephalitis Virus-Like Particle in Complex with SKE26 Fab
    • Complex: SKE26 Fab
    • Virus: Eastern equine encephalitis virus
KeywordsEastern Equine Encephalitis virus / Virus-Like Particle / virus-fab complex / VIRUS LIKE PARTICLE
Biological speciesMacaca fascicularis (crab-eating macaque) / Eastern equine encephalitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsPletnev S / Verardi R / Roedeger M / Kwong P
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 12, 2022-
Header (metadata) releaseSep 20, 2023-
Map releaseSep 20, 2023-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28117.png

Downloads & links

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Map

FileDownload / File: emd_28117.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.66 Å/pix.
x 700 pix.
= 1162. Å		1.66 Å/pix.
x 700 pix.
= 1162. Å		1.66 Å/pix.
x 700 pix.
= 1162. Å

Surface

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Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.24632452 - 1.0849663
Average (Standard dev.)-0.00039257485 (±0.078319654)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions700700700
Spacing700700700
CellA=B=C: 1162.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_28117_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_28117_half_map_2.map
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Eastern Equine Encephalitis Virus-Like Particle in Complex with S...

EntireName: Eastern Equine Encephalitis Virus-Like Particle in Complex with SKE26 Fab
Components
  • Complex: Eastern Equine Encephalitis Virus-Like Particle in Complex with SKE26 Fab
    • Complex: SKE26 Fab
    • Virus: Eastern equine encephalitis virus

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Supramolecule #1: Eastern Equine Encephalitis Virus-Like Particle in Complex with S...

SupramoleculeName: Eastern Equine Encephalitis Virus-Like Particle in Complex with SKE26 Fab
type: complex / ID: 1 / Parent: 0

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Supramolecule #3: SKE26 Fab

SupramoleculeName: SKE26 Fab / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Macaca fascicularis (crab-eating macaque)

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Supramolecule #2: Eastern equine encephalitis virus

SupramoleculeName: Eastern equine encephalitis virus / type: virus / ID: 2 / Parent: 1 / NCBI-ID: 11021 / Sci species name: Eastern equine encephalitis virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: Yes

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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 (6k x 4k) / Number real images: 5662 / Average electron dose: 58.06 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 78534
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6xo4

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3) / Number images used: 51190
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3)
Final 3D classificationNumber classes: 7 / Avg.num./class: 8627 / Software - Name: cryoSPARC (ver. 3.3)

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Atomic model buiding 1

Initial modelPDB ID:

6xo4


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL

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