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- PDB-8dec: Cryo-EM Structure of Western Equine Encephalitis Virus -

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Basic information

Entry
Database: PDB / ID: 8dec
TitleCryo-EM Structure of Western Equine Encephalitis Virus
Components
  • Capsid protein
  • Spike glycoprotein E1
  • Spike glycoprotein E2
KeywordsVIRUS LIKE PARTICLE / Western Equine Encephalitis Virus / Virus-Like Particle
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host gene expression / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host gene expression / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / 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 speciesWestern equine encephalitis virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsPletnev, S. / Verardi, R. / Roedeger, M. / Kwong, P.
Funding support United States, 1items
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
DepositionJun 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike glycoprotein E1
B: Spike glycoprotein E2
E: Capsid protein
F: Spike glycoprotein E1
G: Spike glycoprotein E2
I: Capsid protein
J: Spike glycoprotein E1
K: Spike glycoprotein E2
M: Capsid protein
N: Spike glycoprotein E1
O: Spike glycoprotein E2
R: Capsid protein


Theoretical massNumber of molelcules
Total (without water)491,43412
Polymers491,43412
Non-polymers00
Water00
1
A: Spike glycoprotein E1
B: Spike glycoprotein E2
E: Capsid protein
F: Spike glycoprotein E1
G: Spike glycoprotein E2
I: Capsid protein
J: Spike glycoprotein E1
K: Spike glycoprotein E2
M: Capsid protein
N: Spike glycoprotein E1
O: Spike glycoprotein E2
R: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)29,486,016720
Polymers29,486,016720
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Spike glycoprotein E1
B: Spike glycoprotein E2
E: Capsid protein
F: Spike glycoprotein E1
G: Spike glycoprotein E2
I: Capsid protein
J: Spike glycoprotein E1
K: Spike glycoprotein E2
M: Capsid protein
N: Spike glycoprotein E1
O: Spike glycoprotein E2
R: Capsid protein
x 5


  • icosahedral pentamer
  • 2.46 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)2,457,16860
Polymers2,457,16860
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Spike glycoprotein E1
B: Spike glycoprotein E2
E: Capsid protein
F: Spike glycoprotein E1
G: Spike glycoprotein E2
I: Capsid protein
J: Spike glycoprotein E1
K: Spike glycoprotein E2
M: Capsid protein
N: Spike glycoprotein E1
O: Spike glycoprotein E2
R: Capsid protein
x 6


  • icosahedral 23 hexamer
  • 2.95 MDa, 72 polymers
Theoretical massNumber of molelcules
Total (without water)2,948,60272
Polymers2,948,60272
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
Spike glycoprotein E1 / E1 envelope glycoprotein


Mass: 47368.820 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Western equine encephalitis virus / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P13897
#2: Protein
Spike glycoprotein E2 / E2 envelope glycoprotein


Mass: 46374.848 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Western equine encephalitis virus / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P13897
#3: Protein
Capsid protein / Coat protein / C


Mass: 29114.730 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Western equine encephalitis virus / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P13897, togavirin

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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: Western equine encephalitis virus / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Western equine encephalitis virus
Details of virusEmpty: YES / Enveloped: YES / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
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 FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 43.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 2937

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Processing

EM software
IDNameVersionCategory
4cryoSPARC2.15CTF correction
7UCSF Chimera1.14model fitting
9PHENIX1.2model refinement
10cryoSPARC2.15initial Euler assignment
11cryoSPARC2.15final Euler assignment
12cryoSPARC2.15classification
13cryoSPARC2.153D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 15890
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15890 / Symmetry type: POINT
Atomic model buildingSpace: REAL

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