9BAF | pdb_00009baf

Solution NMR structure of conofurin-Delta


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation 3D Report Full Report

Validation slider image for 9BAF

This is version 1.1 of the entry. See complete history

Literature

Design, Synthesis, and Structure-Activity Relationships of Novel Peptide Derivatives of the Severe Acute Respiratory Syndrome-Coronavirus-2 Spike-Protein that Potently Inhibit Nicotinic Acetylcholine Receptors.

Hone, A.J.Santiago, U.Harvey, P.J.Tekarli, B.Gajewiak, J.Craik, D.J.Camacho, C.J.McIntosh, J.M.

(2024) J Med Chem 67: 9587-9598

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c00735
  • Primary Citation Related Structures: 
    9BAF

  • PubMed Abstract: 

    The spike-protein of SARS-CoV-2 has a distinctive amino-acid sequence ( 682 RRARS 686 ) that forms a cleavage site for the enzyme furin. Strikingly, the structure of the spike-protein loop containing the furin cleavage site bears substantial similarity to neurotoxin peptides found in the venoms of certain snakes and marine cone snails. Leveraging this relationship, we designed and synthesized disulfide-constrained peptides with amino-acid sequences corresponding to the furin cleavage-sites of wild-type (B.1 variant) SARS-CoV-2 or the Alpha, Delta, and Omicron variants. Remarkably, some of these peptides potently inhibited α7 and α9α10 nicotinic acetylcholine receptors (nAChR) with nM affinity and showed SARS-CoV-2 variant and nAChR subtype-dependent potencies. Nuclear magnetic resonance spectroscopy and molecular dynamics were used to rationalize structure-activity relationships between peptides and their cognate receptors. These findings delineate nAChR subtypes that can serve as high-affinity spike-protein targets in tissues central to COVID-19 pathophysiology and identify ligands and target receptors to inform the development of novel SARS-CoV-2 therapeutics.


  • Organizational Affiliation
    • School of Biological Sciences, University of Utah, Salt Lake City, Utah 84112, United States.

Macromolecule Content 

  • Total Structure Weight: 1.75 kDa 
  • Atom Count: 118 
  • Modeled Residue Count: 17 
  • Deposited Residue Count: 17 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha-conotoxin LvIA17Conus lividusMutation(s): 1 
UniProt
Find proteins for L8BU87 (Conus lividus)
Explore L8BU87 
Go to UniProtKB:  L8BU87
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL8BU87
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

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: 2024-07-03
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Structure summary