8VSV | pdb_00008vsv

Cryo-EM structure of SINV/EEEV in complex with a potently neutralizing intact human antibody EEEV-373


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 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 elucidation of a unique binding mode by an intact alphavirus human IgG molecule to a quaternary epitope.

Bandyopadhyay, A.Williamson, L.E.Sirohi, D.Bailey, K.Gilliland Jr., T.Klose, T.Buda, G.Trivette, A.Sun, C.Julander, J.G.Klimstra, W.B.Crowe Jr., J.E.Kuhn, R.J.

(2025) Nat Commun 16: 7716-7716

  • DOI: https://doi.org/10.1038/s41467-025-60505-x
  • Primary Citation of Related Structures:  
    8VSV, 9AY1

  • PubMed Abstract: 

    Eastern equine encephalitis virus (EEEV) is a mosquito-transmitted alphavirus that can cause severe encephalitis in humans and horses with a high case fatality rate. There are no licensed EEEV vaccines or therapeutics for human use, warranting the need to better understand the human immune response against EEEV. Here we present a cryo-EM reconstruction of the chimeric virus, Sindbis (SINV)/EEEV, in complex with a potently neutralizing and efficacious intact human IgG1 antibody in a mouse model of infection and disease. This antibody requires bivalency to recognize a quaternary epitope on the E2 glycoprotein and cross-links two virus spikes across the icosahedral two-fold axis through a unique binding mode. Kinetic analysis of the binding interaction provides insights into this distinguishing feature. Mechanistically, the antibody inhibits viral entry into cells through blockade of receptor binding and early fusion events but does not block egress, thereby, exclusively targeting an epitope found on intact virions. The discovery of the quaternary epitope and unique binding mode recognized by this antibody together advance our understanding of the complexity of antibody-antigen interactions and can aid in vaccine design to elicit recognition of distinct epitopes of clinically relevant alphaviruses.


  • Organizational Affiliation
    • Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IgG EEEV-373 Heavy chainA [auth 1],
C [auth 3]
228Homo sapiensMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
IgG EEEV-373 Light chain.B [auth 2],
D [auth 4]
214Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein E1400Eastern equine encephalitis virusMutation(s): 0 
UniProt
Find proteins for W8R5E4 (Eastern equine encephalitis virus)
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Go to UniProtKB:  W8R5E4
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UniProt GroupW8R5E4
Glycosylation
Glycosylation Sites: 1
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
E2 glycoprotein338Eastern equine encephalitis virusMutation(s): 0 
Gene Names: E2
UniProt
Find proteins for A9XR09 (Eastern equine encephalitis virus)
Explore A9XR09 
Go to UniProtKB:  A9XR09
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UniProt GroupA9XR09
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Q [auth G],
R [auth H],
S [auth I],
T [auth J],
U [auth K],
Q [auth G],
R [auth H],
S [auth I],
T [auth J],
U [auth K],
V [auth L]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONScipion

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 StatesU19 AI142790
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI095366

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-11
    Type: Initial release
  • Version 1.1: 2025-12-24
    Changes: Data collection, Database references