9KH7 | pdb_00009kh7

cryo-EM structure of lipase/ligand complex

• PDB DOI: https://doi.org/10.2210/pdb9KH7/pdb
• EM Map EMD-62334: EMDB EMDataResource

• Classification: HYDROLASE
• Organism(s): Acinetobacter baumannii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-11-09 Released: 2025-11-12 
• Deposition Author(s): Lu, D.F., Zhu, D.Y., Liu, S.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural mechanism of 3'3'-cGAMP-induced filamentation and phospholipid hydrolysis by CapV in bacterial antiphage defense.

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.

(2026) Cell Rep 45: 117261-117261

• PubMed: 41984589 
• DOI: https://doi.org/10.1016/j.celrep.2026.117261
• Primary Citation Related Structures: 
  9KH6, 9KH7, 9WN0, 9WN1


• 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.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China.
Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen 518038, China.
School of Bioengineering, Jingchu University of Technology, Jingmen 448000, China.
State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
Biomedical and Health Laboratory in Shanxi Province, Institutes of Biomedical Sciences, Shanxi University, Taiyuan 030006, China.
College of Life Sciences, Shanxi Agricultural University, Taiyuan 030031, China.
Cryo-EM Center, Southern University of Science and Technology, Shenzhen 518055, China.
Department of Natural Product Chemistry, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China. Electronic address: [e-mail].
College of Life Sciences, Shanxi Agricultural University, Taiyuan 030031, China. Electronic address: [e-mail].
Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China; Institute of Medical Sciences, the Second Qilu Hospital of Shandong University, Jinan 250031, China. Electronic address: [e-mail].
Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 225.43 kDa 
• Atom Count: 13,962 
• Modeled Residue Count: 1,758 
• Deposited Residue Count: 1,998 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CBASS cGAMP-activated phospholipase	A, B, C, D, E, F	333	Acinetobacter baumannii	Mutation(s): 0  Gene Names: MKL45_19260

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4BW (Subject of Investigation/LOI)	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	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 C20 H24 N10 O13 P2 RFCBNSCSPXMEBK-INFSMZHSSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): Lu, D.F., Zhu, D.Y., Liu, S.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	--

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release
  
• Version 1.1: 2026-04-29
  Changes: Data collection, Database references