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- PDB-8zr9: Cryo-EM structure of AbCapV filemant bound with 3',3'-cGAMP -

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Basic information

Entry
Database: PDB / ID: 8zr9
TitleCryo-EM structure of AbCapV filemant bound with 3',3'-cGAMP
ComponentsCGAMP-activated phospholipase CapV
KeywordsHYDROLASE / CBASS
Function / homologyPatatin-like phospholipase domain / Patatin-like phospholipase / Patatin-like phospholipase (PNPLA) domain profile. / Acyl transferase/acyl hydrolase/lysophospholipase / lipid catabolic process / hydrolase activity / Chem-4BW / CGAMP-activated phospholipase CapV
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsKong, J.P. / Li, Z.X. / Ke, S.Y. / Xiao, Y.B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2025
Title: Molecular mechanisms of CBASS phospholipase effector CapV mediated membrane disruption.
Authors: Jianping Kong / Wanqian Wu / Shiyue Ke / Zihan Zhou / Shenglan Xia / Jianyu Chen / Runyu Zhu / Yijia Hou / Tinashe Makanyire / Xiangru Shan / Zhuyue Zhuo / Keying Li / Hongtao Shen / Pan ...Authors: Jianping Kong / Wanqian Wu / Shiyue Ke / Zihan Zhou / Shenglan Xia / Jianyu Chen / Runyu Zhu / Yijia Hou / Tinashe Makanyire / Xiangru Shan / Zhuyue Zhuo / Keying Li / Hongtao Shen / Pan Yang / Pingping Huang / Jingxian Liu / Jing Li / Xiaolian Sun / Jiajia Dong / Hongbin Sun / Meirong Chen / Meiling Lu / Zhaoxing Li / Yibei Xiao /
Abstract: Cyclic oligonucleotide-based antiphage signaling systems (CBASS) are widespread bacterial immune systems that trigger host suicide via cyclic nucleotide-activated effectors. The predominant strategy ...Cyclic oligonucleotide-based antiphage signaling systems (CBASS) are widespread bacterial immune systems that trigger host suicide via cyclic nucleotide-activated effectors. The predominant strategy to induce cell death in CBASS is membrane disruption. Here, we demonstrate that patatin-like phospholipase CapV, the most abundant CBASS effector, relocates and cleaves membrane phospholipids at the cell pole upon 3'3'-cGAMP binding, inducing polarized membrane disruption and cell death. Using cryo-EM, we reveal that apo-CapV adopts both dimeric and tetrameric states, with its phospholipid-binding pocket occluded and locked in an inactive conformation. Binding to 3'3'-cGAMP induces filamentation and substantial conformational change of CapV, enhancing membrane binding via electrostatic interactions between its interspaced basic surfaces and the negatively charged phosphate moieties of phospholipids. Simultaneously, the rearrangement opens the phospholipid-binding pocket, enabling the accommodation of two fatty acid chains of phospholipid within distinct hydrophobic pockets. Our findings reveal a filament-dependent activation mechanism for phospholipase-mediated membrane disruption during antiviral response.
History
DepositionJun 4, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CGAMP-activated phospholipase CapV
B: CGAMP-activated phospholipase CapV
C: CGAMP-activated phospholipase CapV
D: CGAMP-activated phospholipase CapV
E: CGAMP-activated phospholipase CapV
F: CGAMP-activated phospholipase CapV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)251,89012
Polymers247,8446
Non-polymers4,0466
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
CGAMP-activated phospholipase CapV


Mass: 41307.312 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: capV, GSE42_04190 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A505MGQ1
#2: Chemical
ChemComp-4BW / 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 / 3',3' cGAMP / c-GMP-AMP / c[G(3',5')pA(3',5')p]


Mass: 674.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C20H24N10O13P2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: AbCapV bound with 3',3'-cGAMP / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 435584 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00217034
ELECTRON MICROSCOPYf_angle_d0.4723016
ELECTRON MICROSCOPYf_dihedral_angle_d22.3322618
ELECTRON MICROSCOPYf_chiral_restr0.0392562
ELECTRON MICROSCOPYf_plane_restr0.0032892

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