8EWF

CryoEM structure of Western equine encephalitis virus VLP in complex with the avian MXRA8 receptor

• PDB DOI: https://doi.org/10.2210/pdb8EWF/pdb
• EM Map EMD-28644: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Chikungunya virus, Anas platyrhynchos
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  MemProtMD


• Deposited: 2022-10-22 Released: 2023-10-25 
• Deposition Author(s): Zimmerman, M.I., Fremont, D.H., Center for Structural Genomics of Infectious Diseases (CSGID), Center for Structural Biology of Infectious Diseases (CSBID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.92 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Alternate domain repeat usage in an alphavirus entry receptor enables host species expansion

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.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A4B4C1 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - B3 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 409.35 kDa 
• Atom Count: 28,665 
• Modelled Residue Count: 3,697 
• Deposited Residue Count: 3,697 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E1 envelope protein	A, D [auth G], F [auth K], H [auth O]	439	Chikungunya virus	Mutation(s): 0  Gene Names: SP, AN927_63007gpSP, AN927_63008gpSP Membrane Entity: Yes
UniProt
Find proteins for Q5XXP3 (Chikungunya virus (strain 37997)) Explore Q5XXP3  Go to UniProtKB:  Q5XXP3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein E2	B [auth C], E [auth I], G [auth M], I [auth Q]	419	Chikungunya virus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q5XXP3 (Chikungunya virus (strain 37997)) Explore Q5XXP3  Go to UniProtKB:  Q5XXP3

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Chimeric MXRA8 receptor: D1 from Duck MXRA8 and D2 from Mouse MXRA8	C [auth E]	265	Anas platyrhynchos	Mutation(s): 0  Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for R0KGK0 (Anas platyrhynchos) Explore R0KGK0  Go to UniProtKB:  R0KGK0
Find proteins for Q9DBV4 (Mus musculus) Explore Q9DBV4  Go to UniProtKB:  Q9DBV4
IMPC:  MGI:1922011
UniProt Groups	R0KGK0Q9DBV4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	J [auth A], K [auth C], L [auth E], M [auth E], N [auth G], O [auth K], P [auth M], Q [auth O], R [auth Q]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.92 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.01

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-10-25 
Deposition Author(s): Zimmerman, M.I., Fremont, D.H., Center for Structural Genomics of Infectious Diseases (CSGID), Center for Structural Biology of Infectious Diseases (CSBID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History  

• Version 1.0: 2023-10-25
  Type: Initial release