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Open data
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Basic information
Entry | Database: PDB / ID: 8s86 | ||||||
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Title | human PLD3 homodimer structure | ||||||
![]() | 5'-3' exonuclease PLD3 | ||||||
![]() | IMMUNE SYSTEM / Exonuclease | ||||||
Function / homology | ![]() 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 | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
![]() | Lammens, K. | ||||||
Funding support | 1items
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![]() | ![]() 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
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 160.1 KB | Display | ![]() |
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PDB format | ![]() | 126 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1011.2 KB | Display | ![]() |
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Full document | ![]() | 1020.1 KB | Display | |
Data in XML | ![]() | 39.1 KB | Display | |
Data in CIF | ![]() | 56.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 19798MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 48058.016 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: PLD3 dimer / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 5.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2900 nm / Nominal defocus min: 1000 nm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 45 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
EM software | Name: EPU / Category: image acquisition | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2823826 / Symmetry type: POINT | ||||||||||||||||||||||||
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