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

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Basic information

Entry
Database: PDB / ID: 8sqn
TitleCryoEM structure of Western equine encephalitis virus VLP in complex with the chimeric Du-D1-Mo-D2 MXRA8 receptor
Components
  • DuD1MoD2 chimeric MXRA8
  • E1 envelope glycoprotein
  • E2 envelope glycoprotein
KeywordsVIRAL PROTEIN/SIGNALING PROTEIN / WEEV / MXRA8 / Receptor / Alphavirus / Avian / VLP / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Structural Genomics of Infectious Diseases / CSGID / VIRAL PROTEIN-SIGNALING PROTEIN complex
Function / homology
Function and homology information


T=4 icosahedral viral capsid / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis ...T=4 icosahedral viral capsid / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / 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
Similarity search - Component
Biological speciesAnas platyrhynchos (mallard)
Western equine encephalitis virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.89 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: Cell / Year: 2023
Title: Vertebrate-class-specific binding modes of the alphavirus receptor MXRA8.
Authors: Ofer Zimmerman / Maxwell I Zimmerman / Saravanan Raju / Christopher A Nelson / John M Errico / Emily A Madden / Autumn C Holmes / Ahmed O Hassan / Laura A VanBlargan / Arthur S Kim / Lucas J ...Authors: Ofer Zimmerman / Maxwell I Zimmerman / Saravanan Raju / Christopher A Nelson / John M Errico / Emily A Madden / Autumn C Holmes / Ahmed O Hassan / Laura A VanBlargan / Arthur S Kim / Lucas J Adams / Katherine Basore / Bradley M Whitener / Sathvik Palakurty / Hannah G Davis-Adams / Chengqun Sun / Theron Gilliland / James T Earnest / Hongming Ma / Gregory D Ebel / Christian Zmasek / Richard H Scheuermann / William B Klimstra / Daved H Fremont / Michael S Diamond /
Abstract: MXRA8 is a receptor for chikungunya (CHIKV) and other arthritogenic alphaviruses with mammalian hosts. However, mammalian MXRA8 does not bind to alphaviruses that infect humans and have avian ...MXRA8 is a receptor for chikungunya (CHIKV) and other arthritogenic alphaviruses with mammalian hosts. However, mammalian MXRA8 does not bind to alphaviruses that infect humans and have avian reservoirs. Here, we show that avian, but not mammalian, MXRA8 can act as a receptor for Sindbis, western equine encephalitis (WEEV), and related alphaviruses with avian reservoirs. Structural analysis of duck MXRA8 complexed with WEEV reveals an inverted binding mode compared with mammalian MXRA8 bound to CHIKV. Whereas both domains of mammalian MXRA8 bind CHIKV E1 and E2, only domain 1 of avian MXRA8 engages WEEV E1, and no appreciable contacts are made with WEEV E2. Using these results, we generated a chimeric avian-mammalian MXRA8 decoy-receptor that neutralizes infection of multiple alphaviruses from distinct antigenic groups in vitro and in vivo. Thus, different alphaviruses can bind MXRA8 encoded by different vertebrate classes with distinct engagement modes, which enables development of broad-spectrum inhibitors.
History
DepositionMay 4, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 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: DuD1MoD2 chimeric MXRA8
B: E1 envelope glycoprotein
D: E2 envelope glycoprotein
F: E1 envelope glycoprotein
H: E2 envelope glycoprotein
J: E1 envelope glycoprotein
L: E2 envelope glycoprotein
N: E1 envelope glycoprotein
P: E2 envelope glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)405,97118
Polymers403,9809
Non-polymers1,9919
Water0
1


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

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Components

#1: Protein DuD1MoD2 chimeric 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)
#2: Protein
E1 envelope glycoprotein / p130 / Structural polyprotein


Mass: 47188.562 Da / Num. of mol.: 4 / Fragment: UNP residues 798-1235
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Western equine encephalitis virus / Production host: Homo sapiens (human) / References: UniProt: Q1W679
#3: Protein
E2 envelope glycoprotein / p130 / Structural polyprotein


Mass: 46171.617 Da / Num. of mol.: 4 / Fragment: UNP residues 321-735
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Western equine encephalitis virus / Production host: Homo sapiens (human) / References: UniProt: Q1W679
#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: Western equine encephalitis virus VLP in complex with a chimeric MXRA8 receptor (Avian D1 with Mammalian D2)
Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES
Molecular weightValue: 7.45 MDa / Experimental value: NO
Source (natural)Organism: Western equine encephalitis 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: 46.45 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: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 431316 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00329244
ELECTRON MICROSCOPYf_angle_d0.57639858
ELECTRON MICROSCOPYf_dihedral_angle_d4.8224043
ELECTRON MICROSCOPYf_chiral_restr0.0454530
ELECTRON MICROSCOPYf_plane_restr0.0055093

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