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- PDB-8eev: Venezuelan equine encephalitis virus-like particle in complex wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8eev | ||||||
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Title | Venezuelan equine encephalitis virus-like particle in complex with Fab SKT-20 | ||||||
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![]() | VIRUS LIKE PARTICLE/IMMUNE SYSTEM / Venezuelan equine encephalitis virus / neutralizing antibody / VEEV / VIRUS LIKE PARTICLE-IMMUNE SYSTEM complex | ||||||
Function / homology | ![]() togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host gene expression / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host gene expression / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / RNA binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||
![]() | Tsybovsky, Y. / Pletnev, S. / Verardi, R. / Roederer, M. / Kwong, P.D. | ||||||
Funding support | 1items
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 567.7 KB | Display | ![]() |
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PDB format | ![]() | 398.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 77.1 KB | Display | |
Data in CIF | ![]() | 121.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 28060MC ![]() 8decC ![]() 8dedC ![]() 8deeC ![]() 8defC ![]() 8deqC ![]() 8derC ![]() 8dulC ![]() 8dunC ![]() 8dwoC ![]() 8eeuC C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 138662.531 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Antibody | Mass: 25421.338 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Cell line (production host): HEK293 / Production host: ![]() #3: Antibody | Mass: 23754.445 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Cell line (production host): HEK293 / Production host: ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Complex between Venezuelan equine encephalitis virus-like particle and Fab SKT20 Type: COMPLEX Details: The map was obtained after symmetry expansion and signal subtraction. Post-processing was performed with DeepEMhancer. Entity ID: all / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 33 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2250 nm / Nominal defocus min: 750 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 47.5 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 680160 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28235 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: BACKBONE TRACE / Space: REAL |