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- PDB-9wn1: PhospholipaseA2 with a ligand -

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Basic information

Entry
Database: PDB / ID: 9wn1
TitlePhospholipaseA2 with a ligand
ComponentsPatatin
KeywordsLIPID BINDING PROTEIN / phospholipasec2 / crystal sturcure / ligand
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 / Chem-4BW / Patatin
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsZhu, D. / Wang, Q.
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
I: Patatin
J: Patatin
K: Patatin
L: Patatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)450,68924
Polymers442,59612
Non-polymers8,09312
Water3,531196
1
A: Patatin
B: Patatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1154
Polymers73,7662
Non-polymers1,3492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-38 kcal/mol
Surface area24180 Å2
MethodPISA
2
C: Patatin
D: Patatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1154
Polymers73,7662
Non-polymers1,3492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-35 kcal/mol
Surface area24720 Å2
MethodPISA
3
E: Patatin
F: Patatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1154
Polymers73,7662
Non-polymers1,3492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-36 kcal/mol
Surface area24780 Å2
MethodPISA
4
G: Patatin
H: Patatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1154
Polymers73,7662
Non-polymers1,3492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-38 kcal/mol
Surface area24600 Å2
MethodPISA
5
I: Patatin
J: Patatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1154
Polymers73,7662
Non-polymers1,3492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-36 kcal/mol
Surface area24540 Å2
MethodPISA
6
K: Patatin
L: Patatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1154
Polymers73,7662
Non-polymers1,3492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-41 kcal/mol
Surface area25080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.956, 159.748, 132.480
Angle α, β, γ (deg.)90.00, 90.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Patatin


Mass: 36882.965 Da / Num. of mol.: 12 / Mutation: K304A
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: 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.: 12 / Source method: obtained synthetically / Formula: C20H24N10O13P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.13 Å3/Da / Density % sol: 42.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 8% PEG6000,0.1M MES 6.0, 0.2M KCL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9791 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Jan 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.76→50 Å / Num. obs: 90466 / % possible obs: 95.5 % / Redundancy: 6.9 % / CC1/2: 0.994 / Net I/σ(I): 7.5
Reflection shellResolution: 2.76→2.91 Å / Num. unique obs: 2802 / CC1/2: 0.774

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Processing

Software
NameVersionClassification
PHENIX(dev_3885: ???)refinement
Aimlessdata scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.76→20.3 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2675 4412 4.89 %
Rwork0.2207 --
obs0.2231 90220 95.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.76→20.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31134 0 540 196 31870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00532462
X-RAY DIFFRACTIONf_angle_d0.97344048
X-RAY DIFFRACTIONf_dihedral_angle_d14.6474212
X-RAY DIFFRACTIONf_chiral_restr0.0554813
X-RAY DIFFRACTIONf_plane_restr0.0075625
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.76-2.790.3911160.32043018X-RAY DIFFRACTION100
2.79-2.830.41581740.31692909X-RAY DIFFRACTION100
2.83-2.860.35041580.29683025X-RAY DIFFRACTION100
2.86-2.90.35031440.29672974X-RAY DIFFRACTION100
2.9-2.930.33341400.28493008X-RAY DIFFRACTION100
2.94-2.980.32581510.27872984X-RAY DIFFRACTION100
2.98-3.020.36681410.27812997X-RAY DIFFRACTION100
3.02-3.060.33251400.27543017X-RAY DIFFRACTION100
3.06-3.110.33581730.2732927X-RAY DIFFRACTION100
3.11-3.160.30291390.27463020X-RAY DIFFRACTION100
3.16-3.220.3641390.26913012X-RAY DIFFRACTION100
3.22-3.270.33611390.26132997X-RAY DIFFRACTION100
3.27-3.340.26511480.24992979X-RAY DIFFRACTION100
3.34-3.40.30321680.24612991X-RAY DIFFRACTION100
3.4-3.480.3159520.27821047X-RAY DIFFRACTION35
3.48-3.560.31841600.24132998X-RAY DIFFRACTION100
3.56-3.650.27761400.23213000X-RAY DIFFRACTION100
3.65-3.740.27941080.22431819X-RAY DIFFRACTION62
3.74-3.850.26331620.2092992X-RAY DIFFRACTION100
3.85-3.980.27051040.21562133X-RAY DIFFRACTION71
3.98-4.120.22561590.20022978X-RAY DIFFRACTION100
4.12-4.280.28021790.1912972X-RAY DIFFRACTION100
4.28-4.470.2211540.18722986X-RAY DIFFRACTION100
4.47-4.710.22291800.17823008X-RAY DIFFRACTION100
4.71-50.2211710.18112944X-RAY DIFFRACTION100
5-5.380.23091300.19623036X-RAY DIFFRACTION100
5.38-5.910.271680.21063003X-RAY DIFFRACTION100
5.91-6.730.21711730.20232992X-RAY DIFFRACTION100
6.73-8.380.23041550.18223015X-RAY DIFFRACTION100
8.39-20.30.19731470.17483027X-RAY DIFFRACTION99

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