+Open data
-Basic information
Entry | Database: PDB / ID: 8s86 | ||||||
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Title | human PLD3 homodimer structure | ||||||
Components | 5'-3' exonuclease PLD3 | ||||||
Keywords | IMMUNE SYSTEM / Exonuclease | ||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
Authors | Lammens, K. | ||||||
Funding support | 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8s86.cif.gz | 160.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8s86.ent.gz | 126 KB | Display | PDB format |
PDBx/mmJSON format | 8s86.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8s86_validation.pdf.gz | 1010.9 KB | Display | wwPDB validaton report |
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Full document | 8s86_full_validation.pdf.gz | 1019.9 KB | Display | |
Data in XML | 8s86_validation.xml.gz | 39.1 KB | Display | |
Data in CIF | 8s86_validation.cif.gz | 56.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s8/8s86 ftp://data.pdbj.org/pub/pdb/validation_reports/s8/8s86 | HTTPS FTP |
-Related structure data
Related structure data | 19798MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Gene: PLD3 / Production host: Homo sapiens (human) / References: UniProt: Q8IV08, spleen exonuclease |
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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 |
-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: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 5.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
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) |
-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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