9L1N | pdb_00009l1n

Structure of Western equine encephalitis virus 71V1658 strain VLP in complex with human PCDH10 EC1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structural basis for the recognition of two different types of receptors by Western equine encephalitis virus.

Ma, B.Cao, Z.Ding, W.Zhang, X.Xiang, Y.Cao, D.

(2025) Cell Rep 44: 115724-115724

  • DOI: https://doi.org/10.1016/j.celrep.2025.115724
  • Primary Citation of Related Structures:  
    9L1N, 9L99, 9L9A

  • PubMed Abstract: 

    Western equine encephalitis virus (WEEV) enters cells via various receptors. Here, we report the cryoelectron microscopy (cryo-EM) structures of WEEV in complex with its receptors PCDH10 and very-low-density lipoprotein receptor (VLDLR). Structural analysis shows that PCDH10 binds in the cleft formed by adjacent E2-E1 heterodimers of WEEV through its EC1 ectodomain. Residues of viral envelope proteins involved in the interactions with PCDH10 EC1 are unique to WEEV. The strain-specific receptor VLDLR binds WEEV strain McMillan through two consecutive ecto-LDLR class A (LA) repeats. LA1-2, LA2-3, LA3-4, LA4-5, and LA5-6 of VLDLR all have detectable interactions with WEEV. Detailed structures of WEEV in complex with LA1-2 and LA2-3 show that the N-terminal LA repeat binds in the cleft and that the C-terminal LA repeat is attached to the E2 B domain. The acquisition of a single E2 mutation (V265F) allows WEEV strain 71V-1658, originally unable to bind VLDLR, to gain this receptor-binding ability. The binding of VLDLR to WEEV is in a mode different from those of other alphaviruses.


  • Organizational Affiliation

    Beijing Frontier Research Center for Biological Structure, Center for Infectious Disease Research, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, P.R. China; SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Taiyuan 030001, P.R. China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, P.R. China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E1 glycoprotein
A, D, G, J
439Western equine encephalitis virusMutation(s): 0 
UniProt
Find proteins for Q9J1K1 (Western equine encephalitis virus)
Explore Q9J1K1 
Go to UniProtKB:  Q9J1K1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9J1K1
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
E2 glycoprotein
B, E, H, K
416Western equine encephalitis virusMutation(s): 0 
UniProt
Find proteins for Q9J1K1 (Western equine encephalitis virus)
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Go to UniProtKB:  Q9J1K1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9J1K1
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid glycoprotein
C, F, I, L
150Western equine encephalitis virusMutation(s): 0 
UniProt
Find proteins for Q9J1K1 (Western equine encephalitis virus)
Explore Q9J1K1 
Go to UniProtKB:  Q9J1K1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9J1K1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Protocadherin-1095Homo sapiensMutation(s): 0 
Gene Names: PCDH10KIAA1400
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P2E7 (Homo sapiens)
Explore Q9P2E7 
Go to UniProtKB:  Q9P2E7
PHAROS:  Q9P2E7
GTEx:  ENSG00000138650 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P2E7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China--
National Natural Science Foundation of China (NSFC)China--
Chinese Academy of SciencesChina--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-04
    Type: Initial release