+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19798 | |||||||||
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Title | human PLD3 homodimer structure | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Exonuclease / 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 / early 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 / early endosome membrane / late endosome membrane / inflammatory response / Golgi membrane / lysosomal membrane / endoplasmic reticulum membrane / extracellular exosome Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Lammens K | |||||||||
Funding support | 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19798.map.gz | 97 MB | EMDB map data format | |
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Header (meta data) | emd-19798-v30.xml emd-19798.xml | 14 KB 14 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19798_fsc.xml | 9.8 KB | Display | FSC data file |
Images | emd_19798.png | 87.7 KB | ||
Filedesc metadata | emd-19798.cif.gz | 5.4 KB | ||
Others | emd_19798_half_map_1.map.gz emd_19798_half_map_2.map.gz | 95.3 MB 95.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19798 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19798 | HTTPS FTP |
-Validation report
Summary document | emd_19798_validation.pdf.gz | 699.3 KB | Display | EMDB validaton report |
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Full document | emd_19798_full_validation.pdf.gz | 698.9 KB | Display | |
Data in XML | emd_19798_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | emd_19798_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19798 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19798 | HTTPS FTP |
-Related structure data
Related structure data | 8s86MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_19798.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.045 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map B
File | emd_19798_half_map_1.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map A
File | emd_19798_half_map_2.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : PLD3 dimer
Entire | Name: PLD3 dimer |
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Components |
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-Supramolecule #1: PLD3 dimer
Supramolecule | Name: PLD3 dimer / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: 5'-3' exonuclease PLD3
Macromolecule | Name: 5'-3' exonuclease PLD3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: spleen exonuclease |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 48.058016 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 5.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.9 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |