9KH7

cryo-EM structure of lipase/ligand complex

Summary for 9KH7

• Entry DOI: 10.2210/pdb9kh7/pdb
• EMDB information: 62334
• Descriptor: CBASS cGAMP-activated phospholipase, 2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one (2 entities in total)
• Functional Keywords: lipase, hydrolase
• Biological source: Acinetobacter baumannii
• Total number of polymer chains: 6
• Total formula weight: 225428.82

Authors

Lu, D.F.,Zhu, D.Y.,Liu, S. (deposition date: 2024-11-09, release date: 2025-11-12, Last modification date: 2026-04-29)

Primary citation

Lv, Y.,Liu, S.,Wang, Q.,Zhu, J.,Hou, Y.,Xu, H.,Zhu, D.,Liu, Y.,Wu, J.,Wu, C.,Shang, G.,Lou, H.,Lu, D.,Yuan, H.,Zhu, D.
Structural mechanism of 3'3'-cGAMP-induced filamentation and phospholipid hydrolysis by CapV in bacterial antiphage defense.
Cell Rep, 45:117261-117261, 2026

PubMed Abstract: The cyclic-oligonucleotide-based antiphage signaling system (CBASS) protects bacteria from phage infection. In Vibrio cholerae, phage infection activates CD-NTase DncV to produce 3'3'-cGAMP, which triggers phospholipase CapV to degrade phosphatidylethanolamine and phosphatidylglycerol, the major phospholipids in the inner-membranes, thereby inducing cell death. However, how 3'3'-cGAMP activates CapV was unclear. Here we present crystal structures of inactive Acinetobacter baumannii CapV in apo and 3'3'-cGAMP-bound forms, along with cryo-EM structures of activated CapV-3'3'-cGAMP complex, with or without substrate dioleoylphosphatidyl-ethanolamine (DOPE). Apo-CapV forms symmetric dimers in a "closed" state. 3'3'-cGAMP binding drives lateral polymerization of dimers into filament assembly, inducing an "open" state that exposes the active site and substrate-binding cleft. DOPE binding further shifts CapV to an "ajar" state, where a Y-shaped cleft positions DOPE for hydrolysis via a conserved Ser/Asp catalytic dyad. This 3'3'-cGAMP-induced filamentation mirrors activation mechanisms of TIR-STING, TIR-SAVED, and mammalian STING, revealing a conserved signaling pattern across immune systems.

PubMed: 41984589
DOI: 10.1016/j.celrep.2026.117261

Experimental method

ELECTRON MICROSCOPY (3 Å)