8B6N | pdb_00008b6n

X-ray structure of the haloalkane dehalogenase HaloTag7 circular permutated at positions 141-156 (cpHaloTagDelta)

• PDB DOI: https://doi.org/10.2210/pdb8B6N/pdb

• Classification: HYDROLASE
• Organism(s): Rhodococcus sp. (in: high G+C Gram-positive bacteria)
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-09-27 Released: 2023-10-11 
• Deposition Author(s): Tarnawski, M., Johnsson, K., Hiblot, J.
• Funding Organization(s): Max Planck Society

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.250 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

Recording physiological history of cells with chemical labeling.

Huppertz, M.C., Wilhelm, J., Grenier, V., Schneider, M.W., Falt, T., Porzberg, N., Hausmann, D., Hoffmann, D.C., Hai, L., Tarnawski, M., Pino, G., Slanchev, K., Kolb, I., Acuna, C., Fenk, L.M., Baier, H., Hiblot, J., Johnsson, K.

(2024) Science 383: 890-897

• PubMed: 38386755 
• DOI: https://doi.org/10.1126/science.adg0812
• Primary Citation Related Structures: 
  8B6N, 8B6P


• PubMed Abstract: 
  

  Recordings of the physiological history of cells provide insights into biological processes, yet obtaining such recordings is a challenge. To address this, we introduce a method to record transient cellular events for later analysis. We designed proteins that become labeled in the presence of both a specific cellular activity and a fluorescent substrate. The recording period is set by the presence of the substrate, whereas the cellular activity controls the degree of the labeling. The use of distinguishable substrates enabled the recording of successive periods of activity. We recorded protein-protein interactions, G protein-coupled receptor activation, and increases in intracellular calcium. Recordings of elevated calcium levels allowed selections of cells from heterogeneous populations for transcriptomic analysis and tracking of neuronal activities in flies and zebrafish.

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Organizational Affiliation: 
• Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.
Department Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence, Am Klopferspitz 18, 82152 Martinsried, Germany.
Active Sensing, Max Planck Institute for Biological Intelligence, Am Klopferspitz 18, 82152 Martinsried, Germany.
Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany.
Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.
Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
Protein Expression and Characterization Facility, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.
Chica and Heinz Schaller Foundation, Institute of Anatomy and Cell Biology, Heidelberg University, Im Neuenheimer Feld 307, 69120 Heidelberg, Germany.
GENIE Project Team, Janelia Research Campus, Ashburn, VA 20147, USA.
Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.

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: 32.78 kDa 
• Atom Count: 2,189 
• Modeled Residue Count: 272 
• Deposited Residue Count: 294 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haloalkane dehalogenase	A	294	Rhodococcus sp. (in: high G+C Gram-positive bacteria)	Mutation(s): 0  Gene Names: dhaA EC: 3.8.1.5
UniProt
Find proteins for P0A3G3 (Rhodococcus sp) Explore P0A3G3  Go to UniProtKB:  P0A3G3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NHE	B [auth A]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C8 H17 N O3 S MKWKNSIESPFAQN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.250 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.85	α = 90
b = 79.32	β = 90
c = 154.18	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-10-11 
Deposition Author(s): Tarnawski, M., Johnsson, K., Hiblot, J.

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Funding Organization	Location	Grant Number
Max Planck Society	Germany	--

Revision History  

• Version 1.0: 2023-10-11
  Type: Initial release
  
• Version 1.1: 2024-02-14
  Changes: Database references
• Version 1.2: 2024-03-06
  Changes: Database references
• Version 1.3: 2026-03-04
  Changes: Refinement description, Structure summary