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- PDB-8eeu: Venezuelan equine encephalitis virus-like particle in complex wit... -

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Basic information

Entry
Database: PDB / ID: 8eeu
TitleVenezuelan equine encephalitis virus-like particle in complex with Fab SKT05
Components
  • Coat protein
  • Fab SKT05 heavy chain
  • Fab SKT05 light chain
KeywordsVIRUS LIKE PARTICLE/IMMUNE SYSTEM / Venezuelan equine encephalitis virus / neutralizing antibody / VEEV / VIRUS LIKE PARTICLE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / symbiont-mediated suppression of host gene expression / 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 toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / symbiont-mediated suppression of host gene expression / 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 / virion membrane / structural molecule activity / proteolysis / RNA binding / membrane
Similarity search - Function
Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein ...Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Structural polyprotein
Similarity search - Component
Biological speciesVenezuelan equine encephalitis virus
Macaca fascicularis (crab-eating macaque)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsTsybovsky, Y. / Pletnev, S. / Verardi, R. / Roederer, M. / Kwong, P.D.
Funding support1items
OrganizationGrant numberCountry
Not funded
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 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coat protein
B: Coat protein
C: Coat protein
D: Coat protein
E: Coat protein
F: Coat protein
H: Fab SKT05 heavy chain
L: Fab SKT05 light chain


Theoretical massNumber of molelcules
Total (without water)880,7328
Polymers880,7328
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Coat protein / p130


Mass: 138662.531 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Venezuelan equine encephalitis virus / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P05674
#2: Antibody Fab SKT05 heavy chain


Mass: 25517.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca fascicularis (crab-eating macaque)
Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Antibody Fab SKT05 light chain


Mass: 23238.729 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca fascicularis (crab-eating macaque)
Cell line (production host): HEK293 / Production host: Homo sapiens (human)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex between Venezuelan equine encephalitis virus-like particle and Fab SKT05
Type: COMPLEX
Details: The map was obtained using symmetry expansion and signal subtraction. DeepEMHancer was used for post-processing.
Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 33 MDa / Experimental value: NO
Source (natural)Organism: Venezuelan equine encephalitis virus
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK 293
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 53.8 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4GctfCTF correction
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 4068840
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 190096
Details: The map was obtained using symmetry expansion and signal subtraction. DeepEMHancer was used for post-processing.
Symmetry type: POINT
Atomic model buildingProtocol: BACKBONE TRACE / Space: REAL

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