8SW8 | pdb_00008sw8

Crystal Structure of HaloTag7 bound to JF669-HaloTag ligand

• PDB DOI: https://doi.org/10.2210/pdb8SW8/pdb

• Classification: HYDROLASE
• Organism(s): Rhodococcus sp. (in: high G+C Gram-positive bacteria)
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-05-17 Released: 2024-06-05 
• Deposition Author(s): Farrants, H., Schreiter, E.R.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.246 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.210 (DCC) 

Starting Model: experimental

Literature

A modular chemigenetic calcium indicator for multiplexed in vivo functional imaging.

Farrants, H., Shuai, Y., Lemon, W.C., Monroy Hernandez, C., Zhang, D., Yang, S., Patel, R., Qiao, G., Frei, M.S., Plutkis, S.E., Grimm, J.B., Hanson, T.L., Tomaska, F., Turner, G.C., Stringer, C., Keller, P.J., Beyene, A.G., Chen, Y., Liang, Y., Lavis, L.D., Schreiter, E.R.

(2024) Nat Methods 21: 1916-1925

• PubMed: 39304767 
• DOI: https://doi.org/10.1038/s41592-024-02411-6
• Primary Citation of Related Structures:  
  8SW8


• PubMed Abstract: 
  

  Genetically encoded fluorescent calcium indicators allow cellular-resolution recording of physiology. However, bright, genetically targetable indicators that can be multiplexed with existing tools in vivo are needed for simultaneous imaging of multiple signals. Here we describe WHaloCaMP, a modular chemigenetic calcium indicator built from bright dye-ligands and protein sensor domains. Fluorescence change in WHaloCaMP results from reversible quenching of the bound dye via a strategically placed tryptophan. WHaloCaMP is compatible with rhodamine dye-ligands that fluoresce from green to near-infrared, including several that efficiently label the brain in animals. When bound to a near-infrared dye-ligand, WHaloCaMP shows a 7× increase in fluorescence intensity and a 2.1-ns increase in fluorescence lifetime upon calcium binding. We use WHaloCaMP1a to image Ca ²⁺ responses in vivo in flies and mice, to perform three-color multiplexed functional imaging of hundreds of neurons and astrocytes in zebrafish larvae and to quantify Ca ²⁺ concentration using fluorescence lifetime imaging microscopy (FLIM).

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Organizational Affiliation: 
• Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA. [e-mail].
Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
Department of Neuroscience, Washington University in St. Louis, St. Louis, MO, USA.
Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.
Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany.
Department of Pharmacology, University of California San Diego, La Jolla, CA, USA.
Department of Electrical and Computer Engineering, Center for BioEngineering, Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, USA.
Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA. [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: 35.29 kDa 
• Atom Count: 2,589 
• Modeled Residue Count: 293 
• Deposited Residue Count: 304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haloalkane dehalogenase	A [auth AAA]	304	Rhodococcus sp. (in: high G+C Gram-positive bacteria)	Mutation(s): 21  Gene Names: dhaA EC: 3.8.1.5
UniProt
Find proteins for P0A3G3 (Rhodococcus sp) Explore P0A3G3  Go to UniProtKB:  P0A3G3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XSR (Subject of Investigation/LOI)	B [auth AAA]	1-[(4aM,10P)-7-(azetidin-1-yl)-10-[2-carboxy-3,4,6-trifluoro-5-({2-[2-(hexyloxy)ethoxy]ethyl}carbamoyl)phenyl]-5,5-dimethyldibenzo[b,e]silin-3(5H)-ylidene]azetidin-1-ium C39 H47 F3 N3 O5 Si ZQPHKFANJCSITK-UHFFFAOYSA-O
CL	C [auth AAA]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.246 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.210 (DCC) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.741	α = 90
b = 62.741	β = 90
c = 163.548	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-05 
Deposition Author(s): Farrants, H., Schreiter, E.R.

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

Revision History  

• Version 1.0: 2024-06-05
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Database references, Structure summary
• Version 1.2: 2024-10-23
  Changes: Database references