7S7V

Crystal structure of iNicSnFR3a Fluorescent Nicotine Sensor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.233 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Fluorescence activation mechanism and imaging of drug permeation with new sensors for smoking-cessation ligands.

Nichols, A.L., Blumenfeld, Z., Fan, C., Luebbert, L., Blom, A.E.M., Cohen, B.N., Marvin, J.S., Borden, P.M., Kim, C.H., Muthusamy, A.K., Shivange, A.V., Knox, H.J., Campello, H.R., Wang, J.H., Dougherty, D.A., Looger, L.L., Gallagher, T., Rees, D.C., Lester, H.A.

(2022) Elife 11

  • DOI: 10.7554/eLife.74648
  • Primary Citation of Related Structures:  
    7S7T, 7S7U, 7S7V

  • PubMed Abstract: 

    • Nicotinic partial agonists provide an accepted aid for smoking cessation and thus contribute to decreasing tobacco-related disease. Improved drugs constitute a continued area of study. However, there remains no reductionist method to examine the cellular and subcellular pharmacokinetic properties of these compounds in living cells ...

    Nicotinic partial agonists provide an accepted aid for smoking cessation and thus contribute to decreasing tobacco-related disease. Improved drugs constitute a continued area of study. However, there remains no reductionist method to examine the cellular and subcellular pharmacokinetic properties of these compounds in living cells. Here, we developed new intensity-based drug-sensing fluorescent reporters (iDrugSnFRs) for the nicotinic partial agonists dianicline, cytisine, and two cytisine derivatives - 10-fluorocytisine and 9-bromo-10-ethylcytisine. We report the first atomic-scale structures of liganded periplasmic binding protein-based biosensors, accelerating development of iDrugSnFRs and also explaining the activation mechanism. The nicotinic iDrugSnFRs detect their drug partners in solution, as well as at the plasma membrane (PM) and in the endoplasmic reticulum (ER) of cell lines and mouse hippocampal neurons. At the PM, the speed of solution changes limits the growth and decay rates of the fluorescence response in almost all cases. In contrast, we found that rates of membrane crossing differ among these nicotinic drugs by >30-fold. The new nicotinic iDrugSnFRs provide insight into the real-time pharmacokinetic properties of nicotinic agonists and provide a methodology whereby iDrugSnFRs can inform both pharmaceutical neuroscience and addiction neuroscience.

    Organizational Affiliation: 

    Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
iNicSnFR 3.0 Fluorescent Nicotine SensorA, B, C, D537Thermoanaerobacter sp. X513Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CRO
Query on CRO		A, B, C, D L-PEPTIDE LINKINGC15 H17 N3 O5THR, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.233 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.189α = 75.72
b = 86.865β = 85.56
c = 91.83γ = 85.28
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United StatesDA037161
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United StatesDA043829
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United StatesGM123582
Tobacco-Related Disease Research Program (TRDRP)United States23XT-0007
Tobacco-Related Disease Research Program (TRDRP)United States27IP-0057

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-13
    Type: Initial release
  • Version 1.1: 2021-11-03
    Changes: Structure summary
  • Version 1.2: 2022-04-27
    Changes: Database references