9V59 | pdb_00009v59

Crystal structure of calcium indicator WHaloCaMP1a labeled with BD566-HTL substrate

PDB DOI: https://doi.org/10.2210/pdb9V59/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Escherichia
Expression System: Escherichia
Mutation(s): No

Deposited: 2025-05-25 Released: 2025-06-11
Deposition Author(s): Zhang, K., Chen, Z.X.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free:
0.255 (Depositor), 0.252 (DCC)
R-Value Work:
0.205 (Depositor), 0.204 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Potential Activation Mechanism of Calcium Indicator WHaloCaMP1a Revealed by the Crystal Structure and Molecular Dynamics Simulations.

Zhang, K., Chen, N., Zhang, J., Chen, Z.

(2025) Biochemistry 64: 4254-4262

PubMed: 41005291 Search on PubMed
DOI: https://doi.org/10.1021/acs.biochem.5c00352
Primary Citation of Related Structures:
9V59

PubMed Abstract:
Chemigenetic indicators combined with advanced organic fluorophores have become increasingly popular in biosensor development due to their integration of protein biocompatibility and the superior optical properties of dyes. However, despite the development of various biosensors based on these systems, the underlying activation mechanisms remain obscure. Here, we report the first crystal structure of the recently developed calcium indicator WHaloCaMP1a in complex with the rhodamine-based fluorophore BD566 _HTL. Integrating structural analysis with molecular dynamics simulations, we identify a potential activation mechanism of WHaloCaMP1a and reveal novel interactions between the sensor and BD566. These findings provide new insights for the rational design of biosensors and the study of protein-dye coevolution.

Organizational Affiliation

College of Future Technology, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China.

Macromolecule Content

Total Structure Weight: 110.18 kDa
Atom Count: 7,736
Modeled Residue Count: 924
Deposited Residue Count: 948
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WHaloCaMP1a	A, B	474	Escherichia	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1EQX Query on A1EQX Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain S [auth B] MOL2 format, chain J [auth A] MOL2 format, chain S [auth B] mmCIF format, chain J [auth A] mmCIF format, chain S [auth B]	J [auth A], S [auth B]	2-[3,6-bis[(1R,5S)-3-oxa-8-azabicyclo[3.2.1]octan-8-yl]-1H-xanthen-9-yl]-4-[2-(2-hexoxyethoxy)ethylcarbamoyl]benzoic acid C₄₃ H₅₃ N₃ O₈ ZBLXNLHFZGTVKZ-WKKVWOBLSA-N		Interactions Focus chain J [auth A] Focus chain S [auth B] Interactions & Density Focus chain J [auth A] Focus chain S [auth B]
GLC (Subject of Investigation/LOI) Query on GLC Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain N [auth B] SDF format, chain L [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain M [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain N [auth B] MOL2 format, chain L [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain M [auth A] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain N [auth B] mmCIF format, chain L [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] L [auth A] M [auth A] C [auth A], D [auth A], E [auth A], L [auth A], M [auth A], N [auth B], U [auth B], V [auth B], W [auth B]	alpha-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-DVKNGEFBSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain G [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] O [auth B] F [auth A], G [auth A], H [auth A], I [auth A], O [auth B], P [auth B], Q [auth B], R [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]
CL (Subject of Investigation/LOI) Query on CL Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain T [auth B] MOL2 format, chain K [auth A] MOL2 format, chain T [auth B] mmCIF format, chain K [auth A] mmCIF format, chain T [auth B]	K [auth A], T [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Focus chain T [auth B] Interactions & Density Focus chain K [auth A] Focus chain T [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free: 0.255 (Depositor), 0.252 (DCC)
R-Value Work: 0.205 (Depositor), 0.204 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.936	α = 90
b = 94.184	β = 101.34
c = 76.041	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-06-11

Deposition Author(s):

Zhang, K.

Chen, Z.X.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	2021YFF0502904
National Natural Science Foundation of China (NSFC)	China	W2412031

Revision History (Full details and data files)

Version 1.0: 2025-06-11
Type: Initial release
Version 1.1: 2025-12-31
Changes: Advisory, Database references, Derived calculations, Structure summary