8EWF | pdb_00008ewf

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


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Vertebrate-class-specific binding modes of the alphavirus receptor MXRA8.

Zimmerman, O.Zimmerman, M.I.Raju, S.Nelson, C.A.Errico, J.M.Madden, E.A.Holmes, A.C.Hassan, A.O.VanBlargan, L.A.Kim, A.S.Adams, L.J.Basore, K.Whitener, B.M.Palakurty, S.Davis-Adams, H.G.Sun, C.Gilliland Jr., T.Earnest, J.T.Ma, H.Ebel, G.D.Zmasek, C.Scheuermann, R.H.Klimstra, W.B.Fremont, D.H.Diamond, M.S.

(2023) Cell 186: 4818-4833.e25

  • DOI: https://doi.org/10.1016/j.cell.2023.09.007
  • Primary Citation of Related Structures:  
    8DAN, 8DAQ, 8EWF, 8SQN

  • PubMed 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 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.


  • Organizational Affiliation
    • Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E1 envelope proteinA,
D [auth G],
F [auth K],
H [auth O]
439Chikungunya virusMutation(s): 0 
Gene Names: SPAN927_63007gpSPAN927_63008gpSP
Membrane Entity: Yes 
UniProt
Find proteins for Q5XXP3 (Chikungunya virus (strain 37997))
Explore Q5XXP3 
Go to UniProtKB:  Q5XXP3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5XXP3
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein E2B [auth C],
E [auth I],
G [auth M],
I [auth Q]
419Chikungunya virusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q5XXP3 (Chikungunya virus (strain 37997))
Explore Q5XXP3 
Go to UniProtKB:  Q5XXP3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5XXP3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Chimeric MXRA8 receptor: D1 from Duck MXRA8 and D2 from Mouse MXRA8C [auth E]265Anas platyrhynchosMutation(s): 0 
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9DBV4 (Mus musculus)
Explore Q9DBV4 
Go to UniProtKB:  Q9DBV4
IMPC:  MGI:1922011
Find proteins for R0KGK0 (Anas platyrhynchos)
Explore R0KGK0 
Go to UniProtKB:  R0KGK0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsR0KGK0Q9DBV4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
J [auth A]
K [auth C]
L [auth E]
M [auth E]
N [auth G]
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:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC4.01

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201700060C

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-25
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-05-21
    Changes: Data collection
  • Version 1.3: 2025-09-24
    Changes: Data collection, Database references