9JHA | pdb_00009jha

X-ray structure of the Haloalkane dehalogenase HaloTag7 labeled with BD626-HTL substrate

• PDB DOI: https://doi.org/10.2210/pdb9JHA/pdb

• Classification: HYDROLASE
• Organism(s): Rhodococcus sp. #1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-09-09 Released: 2025-01-01 
• Deposition Author(s): Zhixing, C., Kecheng, Z.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.225 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

A palette of bridged bicycle-strengthened fluorophores.

Zhang, J., Zhang, K., Wang, K., Wang, B., Zhu, S., Qian, H., Ma, Y., Zhang, M., Liu, T., Chen, P., Shen, Y., Fu, Y., Fang, S., Zhang, X., Zou, P., Deng, W., Mu, Y., Chen, Z.

(2025) Nat Methods 22: 1276-1287

• PubMed: 40389608 
• DOI: https://doi.org/10.1038/s41592-025-02693-4
• Primary Citation Related Structures: 
  9JHA


• PubMed Abstract: 
  

  Organic fluorophores are the keystone of advanced biological imaging. The vast chemical space of fluorophores has been extensively explored in search of molecules with ideal properties. However, within the current molecular constraints, there appears to be a trade-off between high brightness, robust photostability, and tunable biochemical properties. Herein we report a general strategy to systematically boost the performance of donor-acceptor-type fluorophores, such as rhodamines, by leveraging SO ₂ and O-substituted azabicyclo[3.2.1] octane auxochromes. These bicyclic heterocycles give rise to a collection of 'bridged' dyes (BD) spanning the ultraviolet and visible range with top-notch quantum efficiencies, enhanced water solubility, and tunable cell-permeability. Notably, these azabicyclic fluorophores showed remarkable photostability compared to their tetramethyl or azetidine analogs while being completely resistant to oxidative photoblueing. Functionalized BD dyes are tailored for applications in single-molecule imaging, super-resolution imaging (STED and SIM) in fixed or live mammalian and plant cells, and live zebrafish imaging and chemogenetic voltage imaging.

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Organizational Affiliation: 
• College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, State Key Laboratory of Membrane Biology, Peking University, Beijing, China.
Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, China.
College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, China.
College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China.
BSJ Institute, Beijing, China.
PKU-Nanjing Institute of Translational Medicine, Nanjing, China.
Genvivo Biotech, Nanjing, China.
Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China.
ShanghaiTech University, Shanghai, China.
Chinese Institute for Brain Research (CIBR), Beijing, China.
Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China.
University of Chinese Academy of Sciences, Beijing, China.
College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, State Key Laboratory of Membrane Biology, Peking University, Beijing, China. [e-mail].
Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China. [e-mail].
PKU-Nanjing Institute of Translational Medicine, Nanjing, China. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.37 kDa 
• Atom Count: 2,856 
• Modeled Residue Count: 293 
• Deposited Residue Count: 293 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HaloTag	A	293	Rhodococcus sp. #1	Mutation(s): 0  EC: 3.8.1.5
UniProt
Find proteins for P0A3G3 (Rhodococcus sp) Explore P0A3G3  Go to UniProtKB:  P0A3G3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EB6 (Subject of Investigation/LOI)	B [auth A]	4-[2-[2-(6-chloranylhexoxy)ethoxy]ethylcarbamoyl]-2-[10,10-dimethyl-3-[(1~{R},5~{S})-3-oxa-8-azabicyclo[3.2.1]octan-8-yl]-6-[(1~{R},5~{S})-3-oxa-8-azoniabicyclo[3.2.1]octan-8-ylidene]anthracen-9-yl]benzoic acid C46 H57 Cl N3 O7 IVNKNENACCYEJS-VKAPFSNZSA-O
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.225 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.696	α = 90
b = 62.696	β = 90
c = 164.386	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-01 
Deposition Author(s): Zhixing, C., Kecheng, Z.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2021YFF0502904

Revision History  

• Version 1.0: 2025-01-01
  Type: Initial release
  
• Version 1.1: 2025-06-25
  Changes: Database references