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- PDB-9wn0: Crystal structure of phospholipase A2 -

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Basic information

Entry
Database: PDB / ID: 9wn0
TitleCrystal structure of phospholipase A2
ComponentsPatatin
KeywordsLIPID BINDING PROTEIN / phospholipase / crystal sturcure / phospholipid
Function / homology: / Patatin-like phospholipase domain / Patatin-like phospholipase / Patatin-like phospholipase (PNPLA) domain profile. / Acyl transferase/acyl hydrolase/lysophospholipase / lipid catabolic process / hydrolase activity / Patatin
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhu, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Rep / Year: 2026
Title: Structural mechanism of 3'3'-cGAMP-induced filamentation and phospholipid hydrolysis by CapV in bacterial antiphage defense.
Authors: Yun Lv / Sheng Liu / Qihai Wang / Jing Zhu / Yingxiang Hou / Haiyan Xu / Deyan Zhu / Yu Liu / Jing Wu / Changxin Wu / Guijun Shang / Hongxiang Lou / Defen Lu / Huiqing Yuan / Deyu Zhu /
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 ...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.
History
DepositionSep 4, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Patatin
B: Patatin
C: Patatin
D: Patatin
E: Patatin
F: Patatin
G: Patatin
H: Patatin


Theoretical massNumber of molelcules
Total (without water)295,5298
Polymers295,5298
Non-polymers00
Water8,539474
1
A: Patatin
B: Patatin


Theoretical massNumber of molelcules
Total (without water)73,8822
Polymers73,8822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-36 kcal/mol
Surface area24600 Å2
MethodPISA
2
C: Patatin
D: Patatin


Theoretical massNumber of molelcules
Total (without water)73,8822
Polymers73,8822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-39 kcal/mol
Surface area24990 Å2
MethodPISA
3
E: Patatin
F: Patatin


Theoretical massNumber of molelcules
Total (without water)73,8822
Polymers73,8822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-40 kcal/mol
Surface area24580 Å2
MethodPISA
4
G: Patatin
H: Patatin


Theoretical massNumber of molelcules
Total (without water)73,8822
Polymers73,8822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-37 kcal/mol
Surface area24660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.010, 86.087, 88.570
Angle α, β, γ (deg.)86.67, 73.37, 86.44
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Patatin


Mass: 36941.066 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: Sequence reference for strain 'Acinetobacter baumannii' is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A4Q7ABV3.
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: EXU28_18015 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4Q7ABV3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 15% PEG1500,0.1M mes 6.0

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9791 Å
DetectorType: APEX II CCD / Detector: CCD / Date: May 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 148596 / % possible obs: 89.7 % / Redundancy: 1.1 % / CC1/2: 0.97 / Net I/σ(I): 8.9
Reflection shellResolution: 2→2.76 Å / Num. unique obs: 7411 / CC1/2: 0.99

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Processing

Software
NameVersionClassification
PHENIX(dev_3885: ???)refinement
Aimlessdata scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→44.64 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 35.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2684 7722 5.2 %
Rwork0.2157 --
obs0.2183 148596 90.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→44.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20840 0 0 474 21314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00821320
X-RAY DIFFRACTIONf_angle_d1.02828832
X-RAY DIFFRACTIONf_dihedral_angle_d10.7772792
X-RAY DIFFRACTIONf_chiral_restr0.0573152
X-RAY DIFFRACTIONf_plane_restr0.0073744
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.43872430.40974621X-RAY DIFFRACTION90
2.02-2.050.4662560.39944445X-RAY DIFFRACTION85
2.05-2.070.45692410.43534468X-RAY DIFFRACTION88
2.07-2.10.45942400.38444854X-RAY DIFFRACTION92
2.1-2.130.3963070.34824741X-RAY DIFFRACTION93
2.13-2.150.41772770.33174771X-RAY DIFFRACTION91
2.15-2.190.3542460.31244768X-RAY DIFFRACTION93
2.19-2.220.35252460.3144814X-RAY DIFFRACTION92
2.22-2.250.42252370.34374612X-RAY DIFFRACTION89
2.25-2.290.3472110.29564719X-RAY DIFFRACTION90
2.29-2.330.32572610.26534738X-RAY DIFFRACTION91
2.33-2.370.32362710.25114693X-RAY DIFFRACTION91
2.37-2.420.35322750.25644612X-RAY DIFFRACTION90
2.42-2.470.33462730.25134494X-RAY DIFFRACTION87
2.47-2.520.3442500.25594478X-RAY DIFFRACTION87
2.52-2.580.31022980.24454797X-RAY DIFFRACTION94
2.58-2.640.3382820.24354832X-RAY DIFFRACTION93
2.64-2.710.2732890.24344724X-RAY DIFFRACTION92
2.71-2.790.29362610.23034857X-RAY DIFFRACTION93
2.79-2.880.27272700.22424821X-RAY DIFFRACTION93
2.88-2.990.29022630.22874753X-RAY DIFFRACTION92
2.99-3.110.29722490.22544635X-RAY DIFFRACTION90
3.11-3.250.31362430.22244353X-RAY DIFFRACTION84
3.25-3.420.24952560.21154839X-RAY DIFFRACTION93
3.42-3.630.25182600.19814831X-RAY DIFFRACTION93
3.63-3.910.24262240.18144873X-RAY DIFFRACTION93
3.91-4.310.19432320.16184725X-RAY DIFFRACTION91
4.31-4.930.18982470.14524390X-RAY DIFFRACTION85
4.93-6.210.20382340.17214971X-RAY DIFFRACTION95
6.21-44.640.17352800.14724645X-RAY DIFFRACTION90

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