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- EMDB-67105: The structure of PldB-PA5088 complex state_1 -

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Basic information

Entry
Database: EMDB / ID: EMD-67105
TitleThe structure of PldB-PA5088 complex state_1
Map data
Sample
  • Complex: Complex of Pldb-PA5088
    • Protein or peptide: PLD phosphodiesterase domain-containing protein
    • Protein or peptide: Sel1 repeat family protein
KeywordsInhibitor / Complex / IMMUNE SYSTEM
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsYang JW / Yang XY / Li ZQ
Funding support China, 1 items
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 17, 2025-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_67105.png

Downloads & links

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Map

FileDownload / File: emd_67105.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.67 Å/pix.
x 288 pix.
= 192.384 Å		0.67 Å/pix.
x 288 pix.
= 192.384 Å		0.67 Å/pix.
x 288 pix.
= 192.384 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.668 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0961
Minimum - Maximum-0.20484175 - 0.45175332
Average (Standard dev.)0.00033534353 (±0.019413926)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 192.384 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_67105_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_67105_half_map_2.map
Projections & Slices
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Sample components

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Entire : Complex of Pldb-PA5088

EntireName: Complex of Pldb-PA5088
Components
  • Complex: Complex of Pldb-PA5088
    • Protein or peptide: PLD phosphodiesterase domain-containing protein
    • Protein or peptide: Sel1 repeat family protein

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Supramolecule #1: Complex of Pldb-PA5088

SupramoleculeName: Complex of Pldb-PA5088 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)

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Macromolecule #1: PLD phosphodiesterase domain-containing protein

MacromoleculeName: PLD phosphodiesterase domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 80.928703 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: TLDWFANKAF YPPRAGVHIK PLINGQAAFD AVHAAMEAAR HSIDIITWGF DPAMRFKRPD GPRIGELLQT KGREGVQARV LVWSNQLAR LKENTIPGAG VGGSGGTWAG SGVASGSAVD NEVLRLEQRR QHNLNLIARQ QEALERSERL HREGRLPSFD P RGAAHARA ...String:
TLDWFANKAF YPPRAGVHIK PLINGQAAFD AVHAAMEAAR HSIDIITWGF DPAMRFKRPD GPRIGELLQT KGREGVQARV LVWSNQLAR LKENTIPGAG VGGSGGTWAG SGVASGSAVD NEVLRLEQRR QHNLNLIARQ QEALERSERL HREGRLPSFD P RGAAHARA RIAELEAENA EIQRTLDSSE AQGYGGKRGS GGTRQDPWGQ IFTRDWFKAV RGGGLQNVEF RTRDFEQTAR PV MNGEQVR LVNGRLQSLI HLLRADGNDD LGIGQLLVLT QFASHHQKMV LVDYGSPQAI GFVMGHNMHR NYWDTSAHLF DDR AAGRDP GFGPWQDISM QVQGPVLADL SRNFSEAWDL ETPWYKRWFS TPSLTAERDA LPLPKIATPA SNSVAQICRT QPQD DERSI LEHYLKALGN ATDYVYMENQ YFRYAGFAER LRKTAQVRKA RGVPGDLYLF VVTNTPDSSD ASKTTYDMMK GLGQE QLMP QVQRDLAHDL REKREQLKQV RENLHPDPYV RRGQENNIER LERKIEALEE KGVTPEVEQR LGDLGAQEIP GLAKNT GED DKPYQLAEAP GLKVVVATLA TSDPAPGSPP PARLSAEAEA ALGAPPLKAR YKHIYVHSKL LLVDDLYTLL SSANINV RS MHGDSELGIA QPNPDLARAM REELWGAHVG RLAETTEKNF ELWNQKMDDN WKAQVADEPF TSHLLRFWDV TTPYSQNL T VD

UniProtKB: PLD phosphodiesterase domain-containing protein

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Macromolecule #2: Sel1 repeat family protein

MacromoleculeName: Sel1 repeat family protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 30.509408 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AELRPFICVN EKDHLPSLDP QADAWYREAV ALAKPDTLRP WDRIVDLYSK AVERGHWKAM HNLASLYRTG WPGGVEKDTQ KALDLYQKM IDLKVPQGFY DMAAMIGNRA GVKNPATDGL TFLDKAASLG NPPALTELGR LYIYVAGQDE LGLKYTNCAA G QGYAPANY ...String:
AELRPFICVN EKDHLPSLDP QADAWYREAV ALAKPDTLRP WDRIVDLYSK AVERGHWKAM HNLASLYRTG WPGGVEKDTQ KALDLYQKM IDLKVPQGFY DMAAMIGNRA GVKNPATDGL TFLDKAASLG NPPALTELGR LYIYVAGQDE LGLKYTNCAA G QGYAPANY ELAMYYRLVA HNYPKAAGYY LLAASQGNDD AAFFMSGVFD KTSPDVDRMW YAPDEKLHKL YDGIYDQLAA DP DLRFPNL IKDHPLPPHP TQGYDADRPD WKPGQ

UniProtKB: Sel1 repeat family protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 213711
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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