7P5G

NMR structure of a peptide deriving from SARS-CoV-2 S RBD 482-506 fragment in HFIP/H2O


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 38 
  • Selection Criteria: target function 

wwPDB Validation   3D Report Full Report


This is version 2.4 of the entry. See complete history


Literature

Structural analysis of a simplified model reproducing SARS-CoV-2 S RBD/ACE2 binding site.

Buonocore, M.Santoro, A.Grimaldi, M.Covelli, V.Firoznezhad, M.Rodriquez, M.Santin, M.D'Ursi, A.M.

(2022) Heliyon 8: e11568-e11568

  • DOI: https://doi.org/10.1016/j.heliyon.2022.e11568
  • Primary Citation of Related Structures:  
    7P55, 7P5G, 7P5Q, 7P5S

  • PubMed Abstract: 

    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an RNA virus identified as the cause of the coronavirus outbreak in December 2019 (COVID-19). Like all the RNA viruses, SARS-CoV-2 constantly evolves through mutations in its genome, accumulating 1-2 nucleotide changes every month, giving the virus a selective advantage through enhanced transmissibility, greater pathogenicity, and the possibility of circumventing immunity previously acquired by an individual either by natural infection or by vaccination. Several SARS-CoV-2 variants of concern (VoC) have been identified, among which we find Alpha (Lineage B.1.1.7), Beta (Lineage B.1.351), and Gamma (Lineage P.1) variants. Most of the mutations occur in the spike (S) protein, a surface glycoprotein that plays a crucial role in viral infection; the S protein binds the host cell receptor, the angiotensin-converting enzyme of type 2 (ACE2) via the receptor binding domain (RBD) and catalyzes the fusion of the viral membrane with the host cell. In this work, we present the development of a simplified system that would afford to study the change in the SARS-CoV-2 S RBD/ACE2 binding related to the frequent mutations. In particular, we synthesized and studied the structure of short amino acid sequences, mimicking the two proteins' critical portions. Variations in the residues were easily managed through the one-point alteration of the sequences. Nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopies provide insights into ACE2 and SARS-CoV-2 S RBD structure with its related three variants (Alpha, Beta, and Gamma). Spectroscopy data supported by molecular dynamics lead to the description of an ACE2/RBD binding model in which the effect of a single amino acid mutation in changing the binding of S protein to the ACE2 receptor is predictable.


  • Organizational Affiliation

    University of Salerno, Department of Pharmacy, Via Giovanni Paolo II, 132-84084 Fisciano, Salerno, Italy.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein25Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 38 
  • Selection Criteria: target function 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-27
    Type: Initial release
  • Version 2.0: 2022-10-05
    Type: Coordinate replacement
    Reason: Model orientation/position
    Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Experimental preparation, Source and taxonomy, Structure summary
  • Version 2.1: 2022-11-30
    Changes: Database references
  • Version 2.2: 2022-12-07
    Changes: Database references
  • Version 2.3: 2023-06-14
    Changes: Other
  • Version 2.4: 2024-06-19
    Changes: Data collection, Database references