9WPI

Crystal structure of the Sb32-TGP complex

Summary for 9WPI

• Entry DOI: 10.2210/pdb9wpi/pdb
• Descriptor: TGP, Sb32, GLYCEROL, ... (4 entities in total)
• Functional Keywords: antibody; gfp; green fluorescence protein; nanobody; sb32; synthetic nanobody; thermostable green fluorescence protein; tgp, protein binding
• Biological source: Galaxea fascicularis; More
• Total number of polymer chains: 6
• Total formula weight: 128349.08

Authors

Li, D.,Ni, A.,Li, Y.,Gu, W.,Li, T. (deposition date: 2025-09-09, release date: 2026-06-24)

Primary citation

Li, Y.,Gu, W.,Ni, A.,Li, D.,Li, T.
Screening and structural characterization of a nanobody targeting a thermostable green fluorescent protein.
Acta Biochim.Biophys.Sin., Vol.:1-9, 2026

PubMed Abstract: Nanobody-fluorescent protein pairs are powerful tools in imaging, protein purification, and structural biology studies. While thermostable green fluorescent protein (TGP) offers improved characteristics over conventional GFP, nanobodies that specifically recognize TGP remain relatively limited. Here, we report the screening and identification of a synthetic nanobody Sb32 that binds TGP with nanomolar affinity using the ribosome technique. The crystal structure of the Sb32-TGP complex, solved at 1.82 Å resolution, reveals an unusual binding mode in which complementarity determining region 2 (CDR2) provides the major contribution, rather than the typically dominant CDR3. Moreover, the interface is stabilized by an extensive hydration network, which compensates for relatively few direct contacts and may explain the fast association and dissociation kinetics observed for this complex. These findings expand the repertoire of TGP-specific nanobodies and highlight an alternative strategy by which nanobodies achieve high affinity. Sb32 provides a new reagent for TGP-based applications, with potential utility in membrane protein purification and structural studies.

PubMed: 42178281
DOI: 10.3724/abbs.2025256

Experimental method

X-RAY DIFFRACTION (1.82 Å)