21DT

X-ray structure of the Haloalkane dehalogenase HaloTag7 labeled with BD566-HTL substrate

This is a non-PDB format compatible entry.

Summary for 21DT

• Entry DOI: 10.2210/pdb21dt/pdb
• Descriptor: Haloalkane dehalogenase, CHLORIDE ION, alpha-D-glucopyranose, ... (5 entities in total)
• Functional Keywords: self-labeling tag, soluble, monomer, fluorescent protein
• Biological source: Escherichia
• Total number of polymer chains: 1
• Total formula weight: 36127.17

Authors

Zhang, K.,Chen, Z. (deposition date: 2025-12-09, release date: 2026-07-08)

Primary citation

Zhang, K.,Zhang, J.,Chen, N.,Chen, Z.
Dynamic conformations of fluorophores on self-labeling protein tags.
Biophys.J., 2026

PubMed Abstract: Self-labeling protein tags (SLPs) enable protein-specific conjugation of synthetic fluorophores for versatile bioimaging, yet their rational engineering has largely relied on static structural models. Here, we reveal that crystal structures of SLP-dye complexes generally bear packing artifacts due to strong π-π interactions of dyes, frequently failing to profile the chromophore microenvironment. By integrating molecular dynamics (MD) with crystallography, we elucidate distinct dynamic behaviors of fluorophores across major SLPs: quasi-free diffusion in SNAP-tag, balanced hydrophobic-polar interactions in TMP-tag, and discrete, state-selective anchoring in HaloTag and Rho-tag. Comparisons with the newly developed SNAP-tag2 demonstrate that functional evolution reshapes conformational landscapes rather than merely strengthening binding. We further validate simulation-derived predictions through MD-guided lattice selection. Together, this work establishes a comparative, dynamic framework for understanding SLP-dye interactions beyond crystallography, while providing a conceptual basis for further engineering chemigenetic tools for advanced imaging and sensing.

PubMed: 42363595
DOI: 10.1016/j.bpj.2026.06.033

Experimental method

X-RAY DIFFRACTION (1.48 Å)