9RTM

X-ray structure of the rhodamine-binding protein tag (Rho-tag) bound to a tetramethylrhodamine ligand

This is a non-PDB format compatible entry.

Summary for 9RTM

• Entry DOI: 10.2210/pdb9rtm/pdb
• Related: 9RTL
• Descriptor: AraC effector-binding domain-containing protein, [9-(2-carboxyphenyl)-6-(dimethylamino)xanthen-3-ylidene]-dimethyl-azanium (3 entities in total)
• Functional Keywords: rhodamine-binding protein, rho-tag, tetramethylrhodamine, unknown function
• Biological source: Chlorobaculum tepidum TLS
• Total number of polymer chains: 2
• Total formula weight: 35467.95

Authors

Tarnawski, M.,Kompa, J.,Johnsson, K. (deposition date: 2025-07-02, release date: 2025-07-30, Last modification date: 2026-08-26)

Primary citation

Kompa, J.,Dornfeld, L.J.,Porzberg, N.,Jang, S.,Zedlitz, S.,Lilje, S.H.,Catapano, C.,Jocher, D.,Merk, L.,Hoege, C.,Mao, R.,Wilhelm, J.,Dietz, M.S.,Tarnawski, M.,Hiblot, J.,Hyman, A.A.,Heilemann, M.,Johnsson, K.
Fast, Bright, and Reversible Fluorescent Labeling of Rhodamine-Binding Proteins.
J.Am.Chem.Soc., 148:1419-1429, 2026

PubMed Abstract: Rhodamine dyes conjugated to targeting ligands can yield exceptionally bright fluorescent probes for live-cell imaging. However, the limited permeability of such rhodamine derivatives restricts their broader applications, particularly . Here, we present Rho-tag and SiR-tag, engineered protein tags derived from bacterial multidrug-resistant proteins that bind unsubstituted (silicon) rhodamines with nanomolar affinity. Unsubstituted (silicon) rhodamines readily cross membranes and enable rapid, reversible, and fluorogenic labeling of the tags in mammalian cells within seconds. The labeling of Rho-tag and SiR-tag is compatible with various super-resolution imaging methods and allows their use alongside self-labeling tags, such as HaloTag7 and SNAP-tag. The high affinity and specificity of both tags, combined with the permeability and outstanding spectroscopic properties of rhodamines, make them particularly attractive for bioimaging, as demonstrated by efficient fluorescent labeling inembryos and zebrafish larvae.

PubMed: 41468521
DOI: 10.1021/jacs.5c18083

Experimental method

X-RAY DIFFRACTION (2.1 Å)