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- PDB-8ewf: CryoEM structure of Western equine encephalitis virus VLP in comp... -

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Basic information

Entry
Database: PDB / ID: 8ewf
TitleCryoEM structure of Western equine encephalitis virus VLP in complex with the avian MXRA8 receptor
Components
  • Chimeric MXRA8 receptor: D1 from Duck MXRA8 and D2 from Mouse MXRA8
  • E1 envelope protein
  • Spike glycoprotein E2
KeywordsVIRAL PROTEIN / WEEV / MXRA8 / Receptor / Alphavirus / Avian / VLP / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Structural Genomics of Infectious Diseases / CSGID / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / 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 ...togavirin / T=4 icosahedral viral capsid / 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 / virion membrane / structural molecule activity / proteolysis / RNA binding / membrane / plasma membrane / cytoplasm
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 / Structural polyprotein
Similarity search - Component
Biological speciesChikungunya virus
Anas platyrhynchos (mallard)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.92 Å
AuthorsZimmerman, M.I. / Fremont, D.H. / Center for Structural Genomics of Infectious Diseases (CSGID) / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: Alternate domain repeat usage in an alphavirus entry receptor enables host species expansion
Authors: Zimmerman, O. / Zimmerman, M.I. / Nelson, C.A. / Raju, S. / Errico, J.M. / Madden, E.A. / Hassan, A.O. / VanBlargan, L.A. / Kim, A.S. / Adams, L.J. / Basore, K. / Whitener, B.M. / Earnest, J. ...Authors: Zimmerman, O. / Zimmerman, M.I. / Nelson, C.A. / Raju, S. / Errico, J.M. / Madden, E.A. / Hassan, A.O. / VanBlargan, L.A. / Kim, A.S. / Adams, L.J. / Basore, K. / Whitener, B.M. / Earnest, J.T. / Holmes, A.C. / Ebel, G.D. / Zmasek, C. / Scheuermann, R.H. / Fremont, D.H. / Diamond, M.S.
History
DepositionOct 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 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: E1 envelope protein
C: Spike glycoprotein E2
E: Chimeric MXRA8 receptor: D1 from Duck MXRA8 and D2 from Mouse MXRA8
G: E1 envelope protein
I: Spike glycoprotein E2
K: E1 envelope protein
M: Spike glycoprotein E2
O: E1 envelope protein
Q: Spike glycoprotein E2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)409,35018
Polymers407,3599
Non-polymers1,9919
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
E1 envelope protein / Structural polyprotein / p130


Mass: 47346.715 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus / Gene: SP, AN927_63007gpSP, AN927_63008gpSP / Production host: Homo sapiens (human) / References: UniProt: A0A1I7PD18
#2: Protein
Spike glycoprotein E2 / E2 envelope glycoprotein


Mass: 46858.312 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus / Production host: Homo sapiens (human) / References: UniProt: Q5XXP3
#3: Protein Chimeric MXRA8 receptor: D1 from Duck MXRA8 and D2 from Mouse MXRA8


Mass: 30539.193 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anas platyrhynchos (mallard) / Production host: Homo sapiens (human)
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY

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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: Chikungunya virus VLP in complex with a chimeric MXRA8 receptor (Avian D1 with Mammalian D2)
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 495 kDa/nm / Experimental value: NO
Source (natural)Organism: Chikungunya virus
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2200 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 1.03 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM softwareName: cryoSPARC / Version: 4.01 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 745448 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00429392
ELECTRON MICROSCOPYf_angle_d0.66640098
ELECTRON MICROSCOPYf_dihedral_angle_d5.0414067
ELECTRON MICROSCOPYf_chiral_restr0.0434574
ELECTRON MICROSCOPYf_plane_restr0.0055165

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