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- PDB-9xqm: The structure of PldB-PA5088 complex state_2 -

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Basic information

Entry
Database: PDB / ID: 9xqm
TitleThe structure of PldB-PA5088 complex state_2
Components
  • PLD phosphodiesterase domain-containing protein
  • Sel1 repeat family protein
KeywordsIMMUNE SYSTEM / Inhibitor / Complex
Function / homology
Function and homology information


phospholipid catabolic process / D-type glycerophospholipase activity
Similarity search - Function
Phospholipase D family / Phospholipase D / : / Sel1 repeat / Phospholipase D. Active site motifs. / Sel1-like repeat / Sel1-like repeats. / Phospholipase D/Transphosphatidylase / Phospholipase D phosphodiesterase active site profile. / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
PLD phosphodiesterase domain-containing protein / Sel1 repeat family protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.56 Å
AuthorsYang, J.W. / Yang, X.Y. / Li, Z.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Commun Biol / Year: 2026
Title: Structural basis of cooperative neutralization of the PldB toxin by immunity proteins in Pseudomonas aeruginosa.
Authors: Xiaoyun Yang / Jiawen Yang / Hong Wang / Xiuhua Liu / Zongqiang Li /
Abstract: PldB, a type VI secretion system-dependent phospholipase D (PLD) effector secreted by multidrug-resistant Pseudomonas aeruginosa, alters host cell membrane permeability and facilitates pathogen ...PldB, a type VI secretion system-dependent phospholipase D (PLD) effector secreted by multidrug-resistant Pseudomonas aeruginosa, alters host cell membrane permeability and facilitates pathogen internalization. Its cytotoxic activity is neutralized by three cognate immunity proteins-PA5086, PA5087, and PA5088-which protect the bacterium from self-intoxication. However, the underlying mechanism remains unclear. Through quantitative and qualitative analyses, we demonstrate that these three immunity proteins function cooperatively to inhibit PldB toxicity. Cryogenic electron microscopy of the PldB-PA5088 complex reveals that PA5088 binds to the HKD2 domain of PldB primarily through electrostatic interactions, markedly reducing the volume of its active center. Interaction studies using domain‑specific truncated PldB variants, together with enzyme activity assays, identify distinct copy numbers and binding regions for PA5086, PA5087, and PA5088 in their association with PldB. Collectively, our findings provide mechanistic insights into immunity protein-mediated neutralization of PldB toxicity, offering a potential foundation for designing PLD-targeting therapeutics against P. aeruginosa infection.
History
DepositionNov 18, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PLD phosphodiesterase domain-containing protein
B: Sel1 repeat family protein


Theoretical massNumber of molelcules
Total (without water)111,4382
Polymers111,4382
Non-polymers00
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 PLD phosphodiesterase domain-containing protein


Mass: 80928.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA14_67220 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2ZIS7
#2: Protein Sel1 repeat family protein


Mass: 30509.408 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA5088 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HU95
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: Complex of Pldb-PA5088 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
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: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
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: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 125617 / Symmetry type: POINT
RefinementHighest resolution: 3.56 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0046126
ELECTRON MICROSCOPYf_angle_d0.778340
ELECTRON MICROSCOPYf_dihedral_angle_d5.265828
ELECTRON MICROSCOPYf_chiral_restr0.044873
ELECTRON MICROSCOPYf_plane_restr0.0061103

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