7ZIZ

X-ray structure of the dead variant haloalkane dehalogenase HaloTag7-D106A bound to a pentanol tetramethylrhodamine ligand (TMR-Hy5)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Exchangeable HaloTag Ligands for Super-Resolution Fluorescence Microscopy.

Kompa, J.Bruins, J.Glogger, M.Wilhelm, J.Frei, M.S.Tarnawski, M.D'Este, E.Heilemann, M.Hiblot, J.Johnsson, K.

(2023) J Am Chem Soc 145: 3075-3083

  • DOI: https://doi.org/10.1021/jacs.2c11969
  • Primary Citation of Related Structures:  
    7ZIY, 7ZIZ, 7ZJ0

  • PubMed Abstract: 

    The specific and covalent labeling of the protein HaloTag with fluorescent probes in living cells makes it a powerful tool for bioimaging. However, the irreversible attachment of the probe to HaloTag precludes imaging applications that require transient binding of the probe and comes with the risk of irreversible photobleaching. Here, we introduce exchangeable ligands for fluorescence labeling of HaloTag (xHTLs) that reversibly bind to HaloTag and that can be coupled to rhodamines of different colors. In stimulated emission depletion (STED) microscopy, probe exchange of xHTLs allows imaging with reduced photobleaching as compared to covalent HaloTag labeling. Transient binding of fluorogenic xHTLs to HaloTag fusion proteins enables points accumulation for imaging in nanoscale topography (PAINT) and MINFLUX microscopy. We furthermore introduce pairs of xHTLs and HaloTag mutants for dual-color PAINT and STED microscopy. xHTLs thus open up new possibilities in imaging across microscopy platforms for a widely used labeling approach.


  • Organizational Affiliation

    Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg 69120, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Haloalkane dehalogenase293Rhodococcus sp. (in: high G+C Gram-positive bacteria)Mutation(s): 22 
Gene Names: dhaA
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
IYL (Subject of Investigation/LOI)
Query on IYL

Download Ideal Coordinates CCD File 
B [auth A][9-[2-carboxy-5-[2-[2-(5-oxidanylpentoxy)ethoxy]ethylcarbamoyl]phenyl]-6-(dimethylamino)xanthen-3-ylidene]-dimethyl-azanium
C34 H42 N3 O7
JWWZUBNFGVWRTE-UHFFFAOYSA-O
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.83α = 90
b = 88.71β = 90
c = 44.2γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-22
    Type: Initial release
  • Version 1.1: 2023-03-01
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description