7S7T | pdb_00007s7t

iNicSnFR3a Nicotine Sensor comprising Periplasmic Binding sequence plus Fluorescent Sequence with varenicline bound

• PDB DOI: https://doi.org/10.2210/pdb7S7T/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Thermoanaerobacter sp. X513
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-09-17 Released: 2021-10-13 
• Deposition Author(s): Fan, C., Shivange, A.V., Looger, L.L., Lester, H.A., Rees, D.C.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA), Tobacco-Related Disease Research Program (TRDRP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.219 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Correction: 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

• PubMed: 36520038 
• DOI: https://doi.org/10.7554/eLife.85479
• Primary Citation Related Structures: 
  7S7T, 7S7U, 7S7V

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 61.3 kDa 
• Atom Count: 4,069 
• Modeled Residue Count: 510 
• Deposited Residue Count: 537 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
iNicSnFR 3.0 Fluorescent Nicotine Sensor	A	537	Thermoanaerobacter sp. X513	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QMR (Subject of Investigation/LOI)	B [auth A]	VARENICLINE C13 H13 N3 JQSHBVHOMNKWFT-DTORHVGOSA-N
IOD	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CRO	A	L-PEPTIDE LINKING	C15 H17 N3 O5		THR, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.219 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 190.366	α = 90
b = 190.366	β = 90
c = 49.742	γ = 120

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
PHENIX	refinement
PHASER	phasing
AutoSol	phasing
Aimless	data scaling
XDS	data reduction
Blu-Ice	data collection

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-10-13 
Deposition Author(s): Fan, C., Shivange, A.V., Looger, L.L., Lester, H.A., Rees, D.C.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)	United States	DA037161
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)	United States	DA043829
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)	United States	GM123582
Tobacco-Related Disease Research Program (TRDRP)	United States	23XT-0007
Tobacco-Related Disease Research Program (TRDRP)	United States	27IP-0057

Revision History  

• 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
• Version 1.3: 2023-02-08
  Changes: Database references
• Version 1.4: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.5: 2023-11-15
  Changes: Data collection
• Version 1.6: 2024-11-13
  Changes: Structure summary
• Version 2.0: 2026-03-18
  Changes: Polymer sequence, Refinement description