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- PDB-9ion: Cryo-EM structure of cUA bound CapE filament -

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Basic information

Entry
Database: PDB / ID: 9ion
TitleCryo-EM structure of cUA bound CapE filament
ComponentscUMP-AMP-activated phospholipase
KeywordsLIPID BINDING PROTEIN / CapE / patatin-like phospholipase protein
Function / homology
Function and homology information


phospholipase A1 / phospholipase A1 activity / lipid catabolic process / fatty acid metabolic process / defense response to virus / membrane
Similarity search - Function
Patatin-like phospholipase domain / Patatin-like phospholipase / Patatin-like phospholipase (PNPLA) domain profile. / Acyl transferase/acyl hydrolase/lysophospholipase
Similarity search - Domain/homology
: / cUMP-AMP-activated phospholipase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsGao, A. / Wang, J.G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell / Year: 2025
Title: Cyclic-dinucleotide-induced filamentous assembly of phospholipases governs broad CBASS immunity.
Authors: Jingge Wang / Zhao Li / Hao Lang / Wenfeng Fu / Yina Gao / Sen Yin / Panpan Sun / Zhaolong Li / Jiafeng Huang / Songqing Liu / Yun Zhu / Fei Sun / Dong Li / Pu Gao / Ang Gao /
Abstract: Cyclic-oligonucleotide-based antiphage signaling systems (CBASS), a widespread antiviral bacterial immune system homologous to the mammalian cGAS-STING pathway, synthesizes cyclic nucleotide signals ...Cyclic-oligonucleotide-based antiphage signaling systems (CBASS), a widespread antiviral bacterial immune system homologous to the mammalian cGAS-STING pathway, synthesizes cyclic nucleotide signals and triggers effector proteins to induce cell death and prevent viral propagation. Among various CBASS effectors, phospholipase effectors are the first to be discovered and are one of the most widespread families that sense cyclic dinucleotides to degrade cell membrane phospholipids. Here, we report that CBASS phospholipases assemble from a dimeric inactive state into active higher-order filamentous oligomers upon sensing cyclic dinucleotides. Using a combined approach of cryo-electron microscopy and X-ray crystallography, we have determined the structures of CBASS phospholipase in the inactive dimeric state, the cyclic-dinucleotide-bound active higher-order state, and the substrate-analog-bound catalytic mimicry state, thereby visualizing the complete conformational reorganization process. Complemented by functional assays of intermolecular binding, phospholipase enzymatic activity, in vitro membrane disruption, and in vivo antiphage efficiency, our work elucidates the mechanisms of assembly and activation of CBASS phospholipases.
History
DepositionJul 9, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cUMP-AMP-activated phospholipase
B: cUMP-AMP-activated phospholipase
C: cUMP-AMP-activated phospholipase
D: cUMP-AMP-activated phospholipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,1698
Polymers141,6284
Non-polymers2,5414
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
cUMP-AMP-activated phospholipase / 3' / 3'-cUAMP receptor CapE / Patatin-like phospholipase


Mass: 35406.938 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: capE / Production host: Escherichia coli (E. coli) / References: UniProt: Q6XGD4, phospholipase A1
#2: Chemical
ChemComp-A1AEP / 3'3'-cUMP-AMP / 1-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxooctahydro-2H,5H,7H,12H-5lambda~5~,12lambda~5~-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]pyrimidine-2,4(1H,3H)-dione


Mass: 635.372 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C19H23N7O14P2
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: CapE / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
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: 1500 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.16_3549: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 249892 / Symmetry type: POINT

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