9DT2 | pdb_00009dt2

Crystal structure of the engineered sulfonylurea repressor EsR (L7-D1), apo form

• PDB DOI: https://doi.org/10.2210/pdb9DT2/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-09-30 Released: 2025-10-08 
• Deposition Author(s): Schreiter, E.R., Leija, C., Kakani, N.K., McBride, K.E., Looger, L.L.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.298 (Depositor), 0.302 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.242 (DCC) 

Starting Model: experimental

Literature

Design and evolution of the tetracycline repressor into sulfonylurea herbicide-responsive gene switches for field crops.

McBride, K.E., Kakani, N.K., Bozhanova, N.G., Fang, J., Lowe, K., Leija, C., McGonigle, B., Schreiter, E.R., Hermanson, F., Chan, M., Arling, M., Wang, N., Cho, H.J., Richey, C., Hoerster, G., Marvin, J.S., Lenderts, B., McReynolds, M.R., Hastings, C., Madrigal, A., Falco, S.C., Lassner, M.W., Anand, A., Gordon-Kamm, W., Looger, L.L.

(2026) Nat Commun 

• PubMed: 42259793 
• DOI: https://doi.org/10.1038/s41467-026-73848-w
• Primary Citation Related Structures: 
  9DT2, 9DT3, 9DT4, 9DT5


• PubMed Abstract: 
  

  Chemically inducible expression systems enable transgene expression regulation in response to external small molecules. Tetracycline repressor (TetR)-based gene switches work in plants, but antibiotics are neither approved nor advisable for crop use. Here we report engineering of TetR mutants that respond to approved sulfonylurea (SU) herbicides instead of antibiotics. Designed variants show low-nanomolar EC ₅₀ values for ethametsulfuron-methyl (Es) or chlorsulfuron and tightly bind the Tet operator sequence, but only in the absence of corresponding SUs. Crystal structures of two repressors in complex with their respective SU ligands reveal extensive interactions explaining their strong binding. The Es repressor-based gene switch is introduced into tobacco, soybean, maize, rice, and Arabidopsis, and robust reporter gene activation is observed upon herbicide application. Addition of a repressor-regulated siRNA targeting the repressor transcript increases the magnitude and spatial distribution of the response following herbicide treatment and results in a partially bistable gene switch. The SU repressors also function well in mammalian cell culture and may enable regulation of additional genes in conjunction with TetR.

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Organizational Affiliation: 
• Research and Development, Corteva Agriscience, Johnston, IA, USA. [e-mail].
Research and Development, Corteva Agriscience, Johnston, IA, USA.
Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA.
Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, USA.
Research and Development, Corteva Agriscience, Johnston, IA, USA. [e-mail].
Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 23.22 kDa 
• Atom Count: 1,365 
• Modeled Residue Count: 175 
• Deposited Residue Count: 208 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sulfonylurea repressor EsR (L7-D1)	A	208	Escherichia coli	Mutation(s): 0  Gene Names:  TetR, teTR, tetR(B), CQ842_25520, D3G36_22370, D3G36_27460, D9E49_27735, D9E49_28675, E5H86_28100, E5H86_30860, EHD79_25975, EHD79_28355, EIZ93_26115, FJQ40_26740, FPI65_29665, FPS11_29235, FPS11_30125, GAJ12_26625, GP965_14335, GP975_09140, GP979_15410, GQM21_16135, GRW05_13910, HIE29_003744, HIE29_005530, HL601_26020, HL601_27135, IPF_209
UniProt
Find proteins for B1VCF0 (Escherichia coli) Explore B1VCF0  Go to UniProtKB:  B1VCF0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.298 (Depositor), 0.302 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.242 (DCC) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.44	α = 90
b = 72.44	β = 90
c = 95.19	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-10-08 
Deposition Author(s): Schreiter, E.R., Leija, C., Kakani, N.K., McBride, K.E., Looger, L.L.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2025-10-08
  Type: Initial release
  
• Version 1.1: 2026-06-24
  Changes: Database references