9L99 | pdb_00009l99

Structure of Western equine encephalitis virus McMillan strain in complex with VLDLR LA1-2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein E1A,
C [auth G]
411Western equine encephalitis virusMutation(s): 0 
UniProt
Find proteins for P13897 (Western equine encephalitis virus)
Explore P13897 
Go to UniProtKB:  P13897
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13897
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein E2B,
D [auth H]
369Western equine encephalitis virusMutation(s): 0 
UniProt
Find proteins for P13897 (Western equine encephalitis virus)
Explore P13897 
Go to UniProtKB:  P13897
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13897
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Very low-density lipoprotein receptorE [auth N]80Homo sapiensMutation(s): 0 
Gene Names: VLDLR
UniProt & NIH Common Fund Data Resources
Find proteins for P98155 (Homo sapiens)
Explore P98155 
Go to UniProtKB:  P98155
PHAROS:  P98155
GTEx:  ENSG00000147852 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP98155
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



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
  • Version 1.1: 2025-07-23
    Changes: Data collection