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- EMDB-32438: The structure of PldA-PA3488 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-32438
TitleThe structure of PldA-PA3488 complex
Map data
Sample
  • Complex: The structure of PldA-PA3488 complex
    • Protein or peptide: Phospholipase D
    • Protein or peptide: Tli4_C domain-containing protein
Function / homology
Function and homology information


phospholipase D activity / phospholipid catabolic process
Similarity search - Function
Tle cognate immunity protein 4, C-terminal domain / Tle cognate immunity protein 4 C-terminal domain / Phospholipase D family / Phospholipase D Active site motif / Phospholipase D. Active site motifs. / Phospholipase D/Transphosphatidylase / Phospholipase D phosphodiesterase active site profile.
Similarity search - Domain/homology
Tle cognate immunity protein 4 C-terminal domain-containing protein / Phospholipase D
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria) / Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsZhao L / Yang XY / Li ZQ
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Nat Commun / Year: 2022
Title: Structural insights into PA3488-mediated inactivation of Pseudomonas aeruginosa PldA.
Authors: Xiaoyun Yang / Zongqiang Li / Liang Zhao / Zhun She / Zengqiang Gao / Sen-Fang Sui / Yuhui Dong / Yanhua Li /
Abstract: PldA, a phospholipase D (PLD) effector, catalyzes hydrolysis of the phosphodiester bonds of glycerophospholipids-the main component of cell membranes-and assists the invasion of the opportunistic ...PldA, a phospholipase D (PLD) effector, catalyzes hydrolysis of the phosphodiester bonds of glycerophospholipids-the main component of cell membranes-and assists the invasion of the opportunistic pathogen Pseudomonas aeruginosa. As a cognate immunity protein, PA3488 can inhibit the activity of PldA to avoid self-toxicity. However, the precise inhibitory mechanism remains elusive. We determine the crystal structures of full-length and truncated PldA and the cryogenic electron microscopy structure of the PldA-PA3488 complex. Structural analysis reveals that there are different intermediates of PldA between the "open" and "closed" states of the catalytic pocket, accompanied by significant conformational changes in the "lid" region and the peripheral helical domain. Through structure-based mutational analysis, we identify the key residues responsible for the enzymatic activity of PldA. Together, these data provide an insight into the molecular mechanisms of PldA invasion and its neutralization by PA3488, aiding future design of PLD-targeted inhibitors and drugs.
History
DepositionDec 21, 2021-
Header (metadata) releaseOct 26, 2022-
Map releaseOct 26, 2022-
UpdateNov 9, 2022-
Current statusNov 9, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32438.png

Downloads & links

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Map

FileDownload / File: emd_32438.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.668 Å
Density
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.15074003 - 0.1642068
Average (Standard dev.)-1.16261535e-05 (±0.0036156976)
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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Sample components

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Entire : The structure of PldA-PA3488 complex

EntireName: The structure of PldA-PA3488 complex
Components
  • Complex: The structure of PldA-PA3488 complex
    • Protein or peptide: Phospholipase D
    • Protein or peptide: Tli4_C domain-containing protein

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Supramolecule #1: The structure of PldA-PA3488 complex

SupramoleculeName: The structure of PldA-PA3488 complex / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Phospholipase D

MacromoleculeName: Phospholipase D / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Molecular weightTheoretical: 122.478062 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLQKKPYNGL HEKELNQINQ QDGSPCVAIS APGCFIKGSN LFSEKRAGNR VRFFTTGRDY FSDLASALDS ASSSIFITGW QVNYDVLLD GRRSLWQCLR QALERSPALK VYVMPWLSPS GSLGTYDFET MLAVFQLNAG LEGGARAFCT PAIQQSDMQG L GVAFSHHQ ...String:
MLQKKPYNGL HEKELNQINQ QDGSPCVAIS APGCFIKGSN LFSEKRAGNR VRFFTTGRDY FSDLASALDS ASSSIFITGW QVNYDVLLD GRRSLWQCLR QALERSPALK VYVMPWLSPS GSLGTYDFET MLAVFQLNAG LEGGARAFCT PAIQQSDMQG L GVAFSHHQ KSVVIDNRIG YVGGIDLAYG RRDDNDFSLD ASGRRGNDAY NPGLPHLGWM AEDEHVSSMG LMMATLFDLS RP LASLTLH APTLRLSPFP HIAASDEPLL SIPLAPSRAR ALNGAAYLSD LFRSPMLPSL QWLGRAYNSS KEGLDEGFER LDA LRRQMV ASSIRAIANL IADNLDALPI EPELERRLRA WLEELRTAAL NLPEALRIKS LLLINQWMSE TELGQVLTLI SGKG FEDIP QNLSGKAGEL AGSLFWTLHR LMQARAGGHQ QPYRYLDEAP QPLASPDNAR LAADQPRMPW QDVHCRIEGP SVYDL ARNF IDRWNGQQAY LAKTPALQDT ALVRSALEAV MKWLNSLAAA AGLENYLDEK RNLRLELDPP TPCWINAPEQ LPQEPE VRR GGMTVQVLRS AAARMLEQEQ AGRLGAGVNL PLQVGVSTEG VQSNCKDAML LAISGAQQFI YIENQFFQSE FGKEGEV FK DLPLSGPMAS LRDVGSLRRD FVVRIRLEEA LEQRDLWLLD WAEVEKIAQE PGTEARQFLK SMLAMWGVNA QGWLTHKL G EAQHGLLNEI GEALARRIER AIQREHPFHV YLVLPVHPEG ALNVPNIMHQ VHLTQQSLVF GEQSLVKRIQ RQMALKALE GKSDPAQARE IIERKDARGR PVYEQQDWSR YLTLLNLRTW AVLGGRVVTE QIYVHSKLLI ADDRVAILGS ANINDRSLQG ERDSELAVM VRDSEPLTVR LDGKNDAIVG KAIHQLRVNL WKKHFGLSQG PGGFVKPASE LSAYLSIPAA QEAWEAIQTL A KENTRAYE RTFNFIPQNI SQTQLQLTPE PPKGFEDGFP ASIWPTWAYR KPGELRAGGQ LMEPMPYQEI FWRSSNLTSV KT FPPPNGV SGFITALPTS WTRGERNDSG LNLSILAHQD SRSLPTQVAM NGDSSAQGKH RT

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Macromolecule #2: Tli4_C domain-containing protein

MacromoleculeName: Tli4_C domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 43.088637 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKRVLMGLIL LSSSNITWAE APSSKYQECL GRMTFEIPEE MEWATYDASR VWQISKGGGH NFTAEVTAVG DNGSYDYDSM IFYVSEKVD KNEFHNASNY IKGTAEIYQD HLRENIKLDK KAISTLQKNK SEEKSIERIK KGIAEMEAKI PLAKIYEHDL G IPDSHILG ...String:
MKRVLMGLIL LSSSNITWAE APSSKYQECL GRMTFEIPEE MEWATYDASR VWQISKGGGH NFTAEVTAVG DNGSYDYDSM IFYVSEKVD KNEFHNASNY IKGTAEIYQD HLRENIKLDK KAISTLQKNK SEEKSIERIK KGIAEMEAKI PLAKIYEHDL G IPDSHILG SKNIPFHVLL WRNQRVYYFT FSKPTENSAQ RIKDLIARFR TRELYEVPNE PGICFPYGFI ADDGKTAYEL KN SLRFTRT PNVIFSLLTA SANDPWQTRP TSGLYDSDFR PGYDRQKWKK SALLDSLHIG KRLAAFEGWR LDPRPDSGER ERA WFGLAH TGGTLDPLVA IQVQTFQKGT DDLTDYTPPP EEVLPRLKAL SQSIEQRLAR

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 577905
FSC plot (resolution estimation)

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