8DAN | pdb_00008dan

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.74 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 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 glycoprotein
A, D, G, J
438Western equine encephalitis virusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q1W679 (Western equine encephalitis virus)
Explore Q1W679 
Go to UniProtKB:  Q1W679
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1W679
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
E2 envelope glycoprotein
B, E, H, K
415Western equine encephalitis virusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q1W679 (Western equine encephalitis virus)
Explore Q1W679 
Go to UniProtKB:  Q1W679
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1W679
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Matrix remodeling-associated protein 8
C, F, I, L
265Asarcornis scutulataMutation(s): 0 
Gene Names: Mxra8ASASCU_R01628
Membrane Entity: Yes 
UniProt
Find proteins for A0A7K7KW08 (Asarcornis scutulata)
Explore A0A7K7KW08 
Go to UniProtKB:  A0A7K7KW08
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7K7KW08
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
M [auth A]
N [auth B]
O [auth C]
P [auth D]
Q [auth E]
M [auth A],
N [auth B],
O [auth C],
P [auth D],
Q [auth E],
R [auth F],
S [auth G],
T [auth H],
U [auth I],
V [auth J],
W [auth K],
X [auth L]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.74 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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: 2023-12-20
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-09-24
    Changes: Data collection, Database references