9JHA | pdb_00009jha

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


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
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • DOI: https://doi.org/10.1038/s41592-025-02693-4
  • Primary Citation of 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.


  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HaloTag293Rhodococcus sp. #1Mutation(s): 0 
EC: 3.8.1.5
UniProt
Find proteins for P0A3G3 (Rhodococcus sp)
Explore P0A3G3 
Go to UniProtKB:  P0A3G3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A3G3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1EB6 (Subject of Investigation/LOI)
Query on A1EB6

Download Ideal Coordinates CCD File 
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
Query on EDO

Download Ideal Coordinates CCD File 
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
Query on CL

Download Ideal Coordinates CCD File 
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 = 62.696α = 90
b = 62.696β = 90
c = 164.386γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2021YFF0502904

Revision History  (Full details and data files)

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