8UA4

Structure of eastern equine encephalitis virus VLP in complex with VLDLR LA1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.58 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 VLDLR recognition by eastern equine encephalitis virus.

Yang, P.Li, W.Fan, X.Pan, J.Mann, C.J.Varnum, H.Clark, L.E.Clark, S.A.Coscia, A.Basu, H.Smith, K.N.Brusic, V.Abraham, J.

(2024) Nat Commun 15: 6548-6548

  • DOI: https://doi.org/10.1038/s41467-024-50887-9
  • Primary Citation of Related Structures:  
    8UA4, 8UA9

  • PubMed Abstract: 

    Eastern equine encephalitis virus (EEEV) is the most virulent alphavirus that infects humans, and many survivors develop neurological sequelae, including paralysis and intellectual disability. Alphavirus spike proteins comprise trimers of heterodimers of glycoproteins E2 and E1 that mediate binding to cellular receptors and fusion of virus and host cell membranes during entry. We recently identified very-low density lipoprotein receptor (VLDLR) and apolipoprotein E receptor 2 (ApoER2) as cellular receptors for EEEV and a distantly related alphavirus, Semliki Forest virus (SFV). Here, we use single-particle cryo-electron microscopy (cryo-EM) to determine structures of the EEEV and SFV spike glycoproteins bound to the VLDLR ligand-binding domain and found that EEEV and SFV interact with the same cellular receptor through divergent binding modes. Our studies suggest that the ability of LDLR-related proteins to interact with viral spike proteins through very small footprints with flexible binding modes results in a low evolutionary barrier to the acquisition of LDLR-related proteins as cellular receptors for diverse sets of viruses.


  • Organizational Affiliation

    Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein E1
A, D, G, J
441Eastern equine encephalitis virusMutation(s): 0 
Gene Names: E1
UniProt
Find proteins for Q88678 (Eastern equine encephalitis virus)
Explore Q88678 
Go to UniProtKB:  Q88678
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ88678
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein E2
B, E, H, K
420Eastern equine encephalitis virusMutation(s): 0 
Gene Names: E2
EC: 3.4.21.90
UniProt
Find proteins for Q88678 (Eastern equine encephalitis virus)
Explore Q88678 
Go to UniProtKB:  Q88678
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ88678
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein
C, F, I, L
261Eastern equine encephalitis virusMutation(s): 1 
UniProt
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Go to UniProtKB:  Q88678
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ88678
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein E3
M, N, O, P
63Eastern equine encephalitis virusMutation(s): 0 
UniProt
Find proteins for P08768 (Eastern equine encephalitis virus)
Explore P08768 
Go to UniProtKB:  P08768
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08768
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Very low-density lipoprotein receptorQ [auth R]36Homo 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
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth N]
BA [auth O]
CA [auth P]
R [auth A]
S [auth B]
AA [auth N],
BA [auth O],
CA [auth P],
R [auth A],
S [auth B],
T [auth D],
U [auth E],
V [auth G],
W [auth H],
X [auth J],
Y [auth K],
Z [auth M]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
DA [auth R]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.58 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Burroughs Wellcome FundUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-14
    Type: Initial release
  • Version 1.1: 2024-08-21
    Changes: Data collection, Database references