9WM9
E.coli beta-galactosidase in complex with fluorescent probe KSS3
This is a non-PDB format compatible entry.
Summary for 9WM9
| Entry DOI | 10.2210/pdb9wm9/pdb |
| Descriptor | Beta-galactosidase, 7-(dimethylamino)-3-[4-[[7-[[4-[2-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]sulfanylethyl]phenyl]amino]-2,1,3-benzoxadiazol-4-yl]sulfonyl]piperazin-1-yl]carbonyl-chromen-2-one, MAGNESIUM ION, ... (4 entities in total) |
| Functional Keywords | beta-galactosidase, fluorescent probe, hydrolase |
| Biological source | Escherichia coli (strain K12) |
| Total number of polymer chains | 4 |
| Total formula weight | 469314.98 |
| Authors | Chen, X.,Ge, Y.H.,Yang, H.,Wang, G.W.,Guo, Y. (deposition date: 2025-09-03, release date: 2026-09-09, Last modification date: 2026-09-23) |
| Primary citation | Wang, G.,Chen, X.,Ge, Y.,Duan, K.,Wu, S.,Qiao, Q.,Shi, D.,Shen, J.W.,Zhang, J.,James, T.D.,Xu, Z.,Guo, Y. Identification of Senescence-Associated beta-Galactosidase With Single-Molecule Resolution. Angew.Chem.Int.Ed.Engl., 2026 Cited by PubMed Abstract: The majority of human senescent cells exhibit overexpression of senescence-associated β-galactosidase (SA-β-gal), rendering this enzyme the most extensively utilized biomarker of senescence and a key prodrug target for intervening in aging. However, strategies for the authentic in situ identification of SA-β-gal with single-molecule resolution have not been established, limiting the accuracy of senescence targeting. Here we present an unprecedented molecular approach to identify SA-β-gal in a manner that avoids dissociation from the target enzyme, which integrates the atomic hybridization of SA-β-gal substrates with protein-environment-sensitive fluorescence technology. Using this design principle, we created nine fluorescent probes with distinct working modes for the single-molecule (target enzyme)-resolved identification of SA-β-gal. Five of them formed crystal complexes with the wild-type β-galactosidase by binding at the active site, clearly evidencing their single-molecule resolution capability. Our strategy, capable of both identifying and locating SA-β-gal, facilitated its application in dynamic single-molecule localization microscopic imaging, achieving the in situ tracking of SA-β-gal in living cells at the nanoscale. Significantly, the probing of SA-β-gal with high fidelity enabled the precise evaluation of the aging degree in mice. As such, our research provides a promising method for the authentic in situ identification of this senescence-associated protein with single-molecule resolution. PubMed: 42666007DOI: 10.1002/anie.5443283 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (3.3 Å) |
Structure validation
No wwPDB Validation report is currently available for this entry.
