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- EMDB-28119: Cryo-EM structure of Antibody SKT05 in complex with Western Equin... -

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Entry
Database: EMDB / ID: EMD-28119
TitleCryo-EM structure of Antibody SKT05 in complex with Western Equine Encephalitis Virus-like Particle
Map data
Sample
  • Organelle or cellular component: Western Equine Encephalitis Virus-like Particle in complex with Antibody Fab SKT05
KeywordsAntibody / SKT05 / Western Equine Encephalitis Virus / broadly neutralizing / IMMUNE SYSTEM
Biological speciesWestern equine encephalitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 5.7 Å
AuthorsCerutti G / 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 12, 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_28119.png

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Map

FileDownload / File: emd_28119.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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AxesZ (Sec.)Y (Row.)X (Col.)
1.66 Å/pix.
x 640 pix.
= 1062.4 Å		1.66 Å/pix.
x 640 pix.
= 1062.4 Å		1.66 Å/pix.
x 640 pix.
= 1062.4 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.66 Å
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Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.13273568 - 0.47581717
Average (Standard dev.)-0.0019283475 (±0.038538564)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 1062.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_28119_half_map_1.map
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AxesZYX

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Half map: #2

Fileemd_28119_half_map_2.map
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Sample components

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Entire : Western Equine Encephalitis Virus-like Particle in complex with A...

EntireName: Western Equine Encephalitis Virus-like Particle in complex with Antibody Fab SKT05
Components
  • Organelle or cellular component: Western Equine Encephalitis Virus-like Particle in complex with Antibody Fab SKT05

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Supramolecule #1: Western Equine Encephalitis Virus-like Particle in complex with A...

SupramoleculeName: Western Equine Encephalitis Virus-like Particle in complex with Antibody Fab SKT05
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Western 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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 46.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 68491
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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