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- EMDB-19798: human PLD3 homodimer structure -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-19798
Titlehuman PLD3 homodimer structure
Map data
Sample
  • Organelle or cellular component: PLD3 dimer
    • Protein or peptide: 5'-3' exonuclease PLD3
KeywordsExonuclease / IMMUNE SYSTEM
Function / homology
Function and homology information


spleen exonuclease / Synthesis of PG / single-stranded DNA 5'-3' DNA exonuclease activity / myotube differentiation / phospholipase D activity / immune system process / regulation of cytokine production involved in inflammatory response / Role of phospholipids in phagocytosis / lysosomal lumen / late endosome membrane ...spleen exonuclease / Synthesis of PG / single-stranded DNA 5'-3' DNA exonuclease activity / myotube differentiation / phospholipase D activity / immune system process / regulation of cytokine production involved in inflammatory response / Role of phospholipids in phagocytosis / lysosomal lumen / late endosome membrane / early endosome membrane / inflammatory response / lysosomal membrane / Golgi membrane / endoplasmic reticulum membrane / extracellular exosome
Similarity search - Function
PLD-like domain / PLD-like domain / Phospholipase D. Active site motifs. / Phospholipase D/Transphosphatidylase / Phospholipase D phosphodiesterase active site profile.
Similarity search - Domain/homology
5'-3' exonuclease PLD3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsLammens K
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Immunity / Year: 2024
Title: Lysosomal endonuclease RNase T2 and PLD exonucleases cooperatively generate RNA ligands for TLR7 activation.
Authors: Marleen Bérouti / Katja Lammens / Matthias Heiss / Larissa Hansbauer / Stefan Bauernfried / Jan Stöckl / Francesca Pinci / Ignazio Piseddu / Wilhelm Greulich / Meiyue Wang / Christophe ...Authors: Marleen Bérouti / Katja Lammens / Matthias Heiss / Larissa Hansbauer / Stefan Bauernfried / Jan Stöckl / Francesca Pinci / Ignazio Piseddu / Wilhelm Greulich / Meiyue Wang / Christophe Jung / Thomas Fröhlich / Thomas Carell / Karl-Peter Hopfner / Veit Hornung /
Abstract: Toll-like receptor 7 (TLR7) is essential for recognition of RNA viruses and initiation of antiviral immunity. TLR7 contains two ligand-binding pockets that recognize different RNA degradation ...Toll-like receptor 7 (TLR7) is essential for recognition of RNA viruses and initiation of antiviral immunity. TLR7 contains two ligand-binding pockets that recognize different RNA degradation products: pocket 1 recognizes guanosine, while pocket 2 coordinates pyrimidine-rich RNA fragments. We found that the endonuclease RNase T2, along with 5' exonucleases PLD3 and PLD4, collaboratively generate the ligands for TLR7. Specifically, RNase T2 generated guanosine 2',3'-cyclic monophosphate-terminated RNA fragments. PLD exonuclease activity further released the terminal 2',3'-cyclic guanosine monophosphate (2',3'-cGMP) to engage pocket 1 and was also needed to generate RNA fragments for pocket 2. Loss-of-function studies in cell lines and primary cells confirmed the critical requirement for PLD activity. Biochemical and structural studies showed that PLD enzymes form homodimers with two ligand-binding sites important for activity. Previously identified disease-associated PLD mutants failed to form stable dimers. Together, our data provide a mechanistic basis for the detection of RNA fragments by TLR7.
History
DepositionMar 5, 2024-
Header (metadata) releaseMay 15, 2024-
Map releaseMay 15, 2024-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19798.png

Downloads & links

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Map

FileDownload / File: emd_19798.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.045 Å
Density
Contour LevelBy AUTHOR: 0.713
Minimum - Maximum-4.2930117 - 7.183138
Average (Standard dev.)-0.0032489242 (±0.09328729)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 313.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map B

Fileemd_19798_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_19798_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PLD3 dimer

EntireName: PLD3 dimer
Components
  • Organelle or cellular component: PLD3 dimer
    • Protein or peptide: 5'-3' exonuclease PLD3

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Supramolecule #1: PLD3 dimer

SupramoleculeName: PLD3 dimer / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 5'-3' exonuclease PLD3

MacromoleculeName: 5'-3' exonuclease PLD3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: spleen exonuclease
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.058016 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: WEYGDLHLFG PNQRPAPCYD PCEAVLVESI PEGLDFPNAS TGNPSTSQAW LGLLAGAHSS LDIASFYWTL TNNDTHTQEP SAQQGEEVL RQLQTLAPKG VNVRIAVSKP SGPQPQADLQ ALLQSGAQVR MVDMQKLTHG VLHTKFWVVD QTHFYLGSAN M DWRSLTQV ...String:
WEYGDLHLFG PNQRPAPCYD PCEAVLVESI PEGLDFPNAS TGNPSTSQAW LGLLAGAHSS LDIASFYWTL TNNDTHTQEP SAQQGEEVL RQLQTLAPKG VNVRIAVSKP SGPQPQADLQ ALLQSGAQVR MVDMQKLTHG VLHTKFWVVD QTHFYLGSAN M DWRSLTQV KELGVVMYNC SCLARDLTKI FEAYWFLGQA GSSIPSTWPR FYDTRYNQET PMEICLNGTP ALAYLASAPP PL CPSGRTP DLKALLNVVD NARSFIYVAV MNYLPTLEFS HPHRFWPAID DGLRRATYER GVKVRLLISC WGHSEPSMRA FLL SLAALR DNHTHSDIQV KLFVVPADEA QARIPYARVN HNKYMVTERA TYIGTSNWSG NYFTETAGTS LLVTQNGRGG LRSQ LEAIF LRDWDSPYSH DLDTSADSVG NACRLL

UniProtKB: 5'-3' exonuclease PLD3

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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: 5.5
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: 2.9 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 45.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: alphafold model
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2823826
FSC plot (resolution estimation)

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