7UVJ

Rationally Designed ED1 Epitope-Scaffold Immunogen for SARS-CoV-2

  • Classification: DE NOVO PROTEIN
  • Organism(s): Escherichia coli
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2022-05-02 Released: 2022-10-12 
  • Deposition Author(s): Yennawar, N.H., Vishweshwaraiah, Y.L., Dokholyan, N.V.
  • Funding Organization(s): National Institutes of Health/Office of the Director, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Passan Foundation, National Institutes of Health/National Institute on Aging (NIH/NIA)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.268 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Adaptation-proof SARS-CoV-2 vaccine design.

Vishweshwaraiah, Y.L.Hnath, B.Rackley, B.Wang, J.Gontu, A.Chandler, M.Afonin, K.A.Kuchipudi, S.V.Christensen, N.Yennawar, N.H.Dokholyan, N.V.

(2022) Adv Funct Mater 32

  • DOI: https://doi.org/10.1002/adfm.202206055
  • Primary Citation of Related Structures:  
    7UVJ

  • PubMed Abstract: 

    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) surface spike glycoprotein - a major antibody target - is critical for virus entry via engagement of human angiotensin-converting enzyme 2 (ACE2) receptor. Despite successes with existing vaccines and therapies that primarily target the receptor binding domain (RBD) of the spike protein, the susceptibility of RBD to mutations provides escape routes for the SARS-CoV-2 from neutralizing antibodies. On the other hand, structural conservation in the spike protein can be targeted to reduce escape mutations and achieve broad protection. Here, we designed candidate stable immunogens that mimic surface features of selected conserved regions of spike protein through 'epitope grafting,' in which we present the target epitope topology on diverse heterologous scaffolds that can structurally accommodate the spike epitopes. Structural characterization of the epitope-scaffolds showed stark agreement with our computational models and target epitopes. The sera from mice immunized with engineered designs display epitope-scaffolds and spike binding activity. We also demonstrated the utility of the designed epitope-scaffolds in diagnostic applications. Taken all together, our study provides important methodology for targeting the conserved, non-RBD structural motifs of spike protein for SARS-CoV-2 epitope vaccine design and demonstrates the potential utility of 'epitope grafting' in rational vaccine design.


  • Organizational Affiliation

    Department of Pharmacology, Penn State College of Medicine, Hershey, PA, 17033-0850, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Apolipoprotein E
A, B
147Escherichia coliMutation(s): 0 
Gene Names: APOE
UniProt & NIH Common Fund Data Resources
Find proteins for P02649 (Homo sapiens)
Explore P02649 
Go to UniProtKB:  P02649
PHAROS:  P02649
GTEx:  ENSG00000130203 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02649
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.268 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.06α = 90
b = 95.631β = 108.576
c = 40.916γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
CrysalisProdata reduction
CrysalisProdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Office of the DirectorUnited StatesOD02858901
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM134864
Passan FoundationUnited States--
National Institutes of Health/National Institute on Aging (NIH/NIA)United StatesAG071675

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-12
    Type: Initial release
  • Version 1.1: 2022-10-19
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-01-17
    Changes: Database references