Crystal structure of a HaloTag-based calcium indicator, HaloCaMP V2, bound to JF635

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


The HaloTag as a general scaffold for far-red tunable chemigenetic indicators.

Deo, C.Abdelfattah, A.S.Bhargava, H.K.Berro, A.J.Falco, N.Farrants, H.Moeyaert, B.Chupanova, M.Lavis, L.D.Schreiter, E.R.

(2021) Nat Chem Biol 17: 718-723

  • DOI: https://doi.org/10.1038/s41589-021-00775-w
  • Primary Citation of Related Structures:  
    6U2M, 6U32

  • PubMed Abstract: 

    Functional imaging using fluorescent indicators has revolutionized biology, but additional sensor scaffolds are needed to access properties such as bright, far-red emission. Here, we introduce a new platform for 'chemigenetic' fluorescent indicators, utilizing the self-labeling HaloTag protein conjugated to environmentally sensitive synthetic fluorophores. We solve a crystal structure of HaloTag bound to a rhodamine dye ligand to guide engineering efforts to modulate the dye environment. We show that fusion of HaloTag with protein sensor domains that undergo conformational changes near the bound dye results in large and rapid changes in fluorescence output. This generalizable approach affords bright, far-red calcium and voltage sensors with highly tunable photophysical and chemical properties, which can reliably detect single action potentials in cultured neurons.

  • Organizational Affiliation

    Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HaloCaMP V2A,
B [auth C]
498Rhodococcus sp. (in: high G+C Gram-positive bacteria)Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PUJ (Subject of Investigation/LOI)
Query on PUJ

Download Ideal Coordinates CCD File 
C [auth A],
I [auth C]
(1E,3S)-1-{10-[2-carboxy-5-({2-[2-(hexyloxy)ethoxy]ethyl}carbamoyl)phenyl]-7-(3-fluoroazetidin-1-yl)-5,5-dimethyldibenz o[b,e]silin-3(5H)-ylidene}-3-fluoroazetidin-1-ium
C39 H48 F2 N3 O5 Si
Query on CA

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
K [auth C]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
K [auth C],
L [auth C],
M [auth C],
N [auth C]
Query on CL

Download Ideal Coordinates CCD File 
D [auth A],
J [auth C]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.56α = 90
b = 60.662β = 91.02
c = 122.6γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2021-04-28
    Changes: Database references
  • Version 1.2: 2021-06-09
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description