7FFF

Structure of Venezuelan equine encephalitis virus with the receptor LDLRAD3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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

Structure of Venezuelan equine encephalitis virus with its receptor LDLRAD3.

Ma, B.Huang, C.Ma, J.Xiang, Y.Zhang, X.

(2021) Nature 598: 677-681

  • DOI: https://doi.org/10.1038/s41586-021-03909-1
  • Primary Citation of Related Structures:  
    7FFE, 7FFF, 7FFL, 7FFN, 7FFO, 7FFQ

  • PubMed Abstract: 

    Venezuelan equine encephalitis virus (VEEV) is an enveloped RNA virus that causes encephalitis and potentially mortality in infected humans and equines 1 . At present, no vaccines or drugs are available that prevent or cure diseases caused by VEEV. Low-density lipoprotein receptor class A domain-containing 3 (LDLRAD3) was recently identified as a receptor for the entry of VEEV into host cells 2 . Here we present the cryo-electron microscopy structure of the LDLRAD3 extracellular domain 1 (LDLRAD3-D1) in complex with VEEV virus-like particles at a resolution of 3.0 Å. LDLRAD3-D1 has a cork-like structure and is inserted into clefts formed between adjacent VEEV E2-E1 heterodimers in the viral-surface trimer spikes through hydrophobic and polar contacts. Mutagenesis studies of LDLRAD3-D1 identified residues that are involved in the key interactions with VEEV. Of note, some of the LDLRAD3-D1 mutants showed a significantly increased binding affinity for VEEV, suggesting that LDLRAD3-D1 may serve as a potential scaffold for the development of inhibitors of VEEV entry. Our structures provide insights into alphavirus assembly and the binding of receptors to alphaviruses, which may guide the development of therapeutic countermeasures against alphaviruses.


  • Organizational Affiliation

    Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, P. R. China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid proteinA [auth K],
B [auth S],
K [auth A],
L [auth F]
275Venezuelan equine encephalitis virus (strain TC-83)Mutation(s): 1 
EC: 3.4.21.90
Membrane Entity: Yes 
UniProt
Find proteins for P05674 (Venezuelan equine encephalitis virus (strain TC-83))
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Go to UniProtKB:  P05674
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05674
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein E1C [auth G],
G [auth B],
M [auth C],
T [auth O]
442Venezuelan equine encephalitis virus (strain TC-83)Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P05674 (Venezuelan equine encephalitis virus (strain TC-83))
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UniProt GroupP05674
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Low-density lipoprotein receptor class A domain-containing protein 3D [auth H],
H [auth D],
N [auth E],
R [auth M]
70Homo sapiensMutation(s): 0 
Gene Names: LDLRAD3LRAD3
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q86YD5 (Homo sapiens)
Explore Q86YD5 
Go to UniProtKB:  Q86YD5
PHAROS:  Q86YD5
GTEx:  ENSG00000179241 
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UniProt GroupQ86YD5
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
assembly protein E3E [auth I],
I [auth T],
O [auth P],
Q [auth L]
59Venezuelan equine encephalitis virus (strain TC-83)Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P05674 (Venezuelan equine encephalitis virus (strain TC-83))
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Go to UniProtKB:  P05674
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UniProt GroupP05674
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein E2F [auth J],
J [auth Q],
P [auth R],
S [auth N]
423Venezuelan equine encephalitis virus (strain TC-83)Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P05674 (Venezuelan equine encephalitis virus (strain TC-83))
Explore P05674 
Go to UniProtKB:  P05674
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UniProt GroupP05674
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-20
    Type: Initial release
  • Version 1.1: 2021-11-17
    Changes: Database references