6EFR | pdb_00006efr

Crystal Structure of iNicSnFR 1.0

PDB DOI: https://doi.org/10.2210/pdb6EFR/pdb

Classification: CHOLINE-BINDING PROTEIN
Organism(s): Thermoanaerobacter sp. X513, Aequorea victoria
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2018-08-17 Released: 2019-01-23
Deposition Author(s): Shivange, A.V., Borden, P.M.
Funding Organization(s): National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.250 (Depositor), 0.251 (DCC)
R-Value Work:
0.188 (Depositor), 0.192 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6EFR

This is version 2.0 of the entry. See complete history.

Literature

Nicotinic Drugs in the Endoplasmic Reticulum: Beginning the Inside-out Pathway of Addiction and Therapy

Shivange, A.V., Borden, P.M., Muthusamy, A.K., Nichols, A.L., Bera, K., Bao, H., Bishara, I., Jeon, J., Mulcahy, M.J., Kim, C.H., Dougherty, D.A., Chapman, E.R., Marvin, J.S., Looger, L.L., Lester, H.A.

(2019) J Gen Physiol

Macromolecule Content

Total Structure Weight: 58.47 kDa
Atom Count: 4,042
Modeled Residue Count: 504
Deposited Residue Count: 520
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
iNicSnFR 1.0, a genetically encoded nicotine biosensor,Green fluorescent protein	A	520	Thermoanaerobacter sp. X513, Aequorea victoria	Mutation(s): 2
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212 Go to UniProtKB: P42212
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P42212
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.250 (Depositor), 0.251 (DCC)
R-Value Work: 0.188 (Depositor), 0.192 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.61	α = 90
b = 95.64	β = 90
c = 151.79	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-01-23

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)	United States	DA037161

Revision History (Full details and data files)

Version 1.0: 2019-01-23
Type: Initial release
Version 1.1: 2019-12-11
Changes: Author supporting evidence
Version 1.2: 2023-10-11
Changes: Data collection, Database references, Refinement description
Version 1.3: 2023-11-15
Changes: Data collection
Version 1.4: 2024-10-16
Changes: Structure summary
Version 2.0: 2026-03-18
Changes: Polymer sequence

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.