7N1H

CryoEM structure of Venezuelan equine encephalitis virus VLP in complex with the LDLRAD3 receptor


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.2 of the entry. See complete history


Literature

Structure of Venezuelan equine encephalitis virus in complex with the LDLRAD3 receptor.

Basore, K.Ma, H.Kafai, N.M.Mackin, S.Kim, A.S.Nelson, C.A.Diamond, M.S.Fremont, D.H.

(2021) Nature 598: 672-676

  • DOI: https://doi.org/10.1038/s41586-021-03963-9
  • Primary Citation of Related Structures:  
    7N1H, 7N1I

  • PubMed Abstract: 

    LDLRAD3 is a recently defined attachment and entry receptor for Venezuelan equine encephalitis virus (VEEV) 1 , a New World alphavirus that causes severe neurological disease in humans. Here we present near-atomic-resolution cryo-electron microscopy reconstructions of VEEV virus-like particles alone and in a complex with the ectodomains of LDLRAD3. Domain 1 of LDLRAD3 is a low-density lipoprotein receptor type-A module that binds to VEEV by wedging into a cleft created by two adjacent E2-E1 heterodimers in one trimeric spike, and engages domains A and B of E2 and the fusion loop in E1. Atomic modelling of this interface is supported by mutagenesis and anti-VEEV antibody binding competition assays. Notably, VEEV engages LDLRAD3 in a manner that is similar to the way that arthritogenic alphaviruses bind to the structurally unrelated MXRA8 receptor, but with a much smaller interface. These studies further elucidate the structural basis of alphavirus-receptor interactions, which could inform the development of therapies to mitigate infection and disease against multiple members of this family.


  • Organizational Affiliation

    Department of Pathology & Immunology, Washington University School of Medicine, St Louis, MO, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Low-density lipoprotein receptor class A domain-containing protein 3A [auth O],
B [auth M],
C [auth N],
D [auth P]
39Mus musculusMutation(s): 0 
Gene Names: Ldlrad3
UniProt
Find proteins for A2AR95 (Mus musculus)
Go to UniProtKB:  A2AR95
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
E1 envelope glycoproteinE [auth D],
H [auth C],
K [auth B],
N [auth A]
442Venezuelan equine encephalitis virusMutation(s): 0 
UniProt
Find proteins for A0A0C4MX98 (Venezuelan equine encephalitis virus)
Go to UniProtKB:  A0A0C4MX98
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
E2 envelope glycoproteinF [auth H],
I [auth G],
L [auth F],
O [auth E]
423Venezuelan equine encephalitis virusMutation(s): 0 
UniProt
Find proteins for A0A0C4MX98 (Venezuelan equine encephalitis virus)
Go to UniProtKB:  A0A0C4MX98
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
CapsidG [auth L],
J [auth K],
M [auth J],
P [auth I]
162Venezuelan equine encephalitis virusMutation(s): 0 
UniProt
Find proteins for A0A0C4MX98 (Venezuelan equine encephalitis virus)
Go to UniProtKB:  A0A0C4MX98
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth E]
U [auth D]
V [auth H]
W [auth C]
AA [auth A],
BA [auth E],
U [auth D],
V [auth H],
W [auth C],
X [auth G],
Y [auth B],
Z [auth F]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
Q [auth O],
R [auth M],
S [auth N],
T [auth P]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1

Structure Validation

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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: 2021-10-13
    Type: Initial release
  • Version 1.1: 2021-10-27
    Changes: Database references
  • Version 1.2: 2021-11-10
    Changes: Database references