7V0O | pdb_00007v0o

Cryo-EM structure of SINV/EEEV in complex with Fab fragment of a moderately/weakly neutralizing human antibody IgG-94


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structural constraints link differences in neutralization potency of human anti-Eastern equine encephalitis virus monoclonal antibodies.

Williamson, L.E.Bandyopadhyay, A.Bailey, K.Sirohi, D.Klose, T.Julander, J.G.Kuhn, R.J.Crowe Jr., J.E.

(2023) Proc Natl Acad Sci U S A 120: e2213690120-e2213690120

  • DOI: https://doi.org/10.1073/pnas.2213690120
  • Primary Citation Related Structures: 
    7V0N, 7V0O, 7V0P

  • PubMed Abstract: 

    Selection and development of monoclonal antibody (mAb) therapeutics against pathogenic viruses depends on certain functional characteristics. Neutralization potency, or the half-maximal inhibitory concentration (IC 50 ) values, is an important characteristic of candidate therapeutic antibodies. Structural insights into the bases of neutralization potency differences between antiviral neutralizing mAbs are lacking. In this report, we present cryo-electron microscopy (EM) reconstructions of three anti-Eastern equine encephalitis virus (EEEV) neutralizing human mAbs targeting overlapping epitopes on the E2 protein, with greater than 20-fold differences in their respective IC 50 values. From our structural and biophysical analyses, we identify several constraints that contribute to the observed differences in the neutralization potencies. Cryo-EM reconstructions of EEEV in complex with these Fab fragments reveal structural constraints that dictate intravirion or intervirion cross-linking of glycoprotein spikes by their IgG counterparts as a mechanism of neutralization. Additionally, we describe critical features for the recognition of EEEV by these mAbs including the epitope-paratope interaction surface, occupancy, and kinetic differences in on-rate for binding to the E2 protein. Each constraint contributes to the extent of EEEV inhibition for blockade of virus entry, fusion, and/or egress. These findings provide structural and biophysical insights into the differences in mechanism and neutralization potencies of these antibodies, which help inform rational design principles for candidate vaccines and therapeutic antibodies for all icosahedral viruses.


  • Organizational Affiliation
    • The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232.

Macromolecule Content 

  • Total Structure Weight: 475.35 kDa 
  • Atom Count: 29,944 
  • Modeled Residue Count: 4,700 
  • Deposited Residue Count: 4,700 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Spike glycoprotein E1
A, B, C, D
400Eastern equine encephalitis virusMutation(s): 0 
UniProt
Find proteins for Q4QXJ7 (Eastern equine encephalitis virus (strain Florida 91-469))
Explore Q4QXJ7 
Go to UniProtKB:  Q4QXJ7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4QXJ7
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
IgG 94 Fab heavy chain
E, G, I, K
222Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
IgG 94 Fab light chain
F, H, J, L
211Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Spike glycoprotein E2M [auth a],
N [auth b],
O [auth c],
P [auth d]
342Eastern equine encephalitis virusMutation(s): 0 
UniProt
Find proteins for Q4QXJ7 (Eastern equine encephalitis virus (strain Florida 91-469))
Explore Q4QXJ7 
Go to UniProtKB:  Q4QXJ7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4QXJ7
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONjspr

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: 2023-04-05
    Type: Initial release
  • Version 1.1: 2024-02-21
    Changes: Data collection, Refinement description, Structure summary
  • Version 1.2: 2024-10-09
    Changes: Data collection, Structure summary