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Yorodumi- PDB-7wm4: Cryo-EM structure of tetrameric TLR3 in complex with dsRNA (90 bp) -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wm4 | ||||||||||||
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Title | Cryo-EM structure of tetrameric TLR3 in complex with dsRNA (90 bp) | ||||||||||||
Components |
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Keywords | IMMUNE SYSTEM/RNA / innate immunity / IMMUNE SYSTEM / IMMUNE SYSTEM-RNA complex | ||||||||||||
Function / homology | Function and homology information type III interferon production / positive regulation of type III interferon production / response to dsRNA / regulation of dendritic cell cytokine production / inflammatory response to wounding / toll-like receptor 3 signaling pathway / necroptotic signaling pathway / positive regulation of cytokine production involved in inflammatory response / positive regulation of macrophage cytokine production / pattern recognition receptor activity ...type III interferon production / positive regulation of type III interferon production / response to dsRNA / regulation of dendritic cell cytokine production / inflammatory response to wounding / toll-like receptor 3 signaling pathway / necroptotic signaling pathway / positive regulation of cytokine production involved in inflammatory response / positive regulation of macrophage cytokine production / pattern recognition receptor activity / toll-like receptor signaling pathway / response to exogenous dsRNA / cellular response to exogenous dsRNA / positive regulation of interferon-alpha production / positive regulation of type I interferon production / cellular response to interferon-beta / positive regulation of chemokine production / extrinsic apoptotic signaling pathway / JNK cascade / positive regulation of interleukin-12 production / positive regulation of interferon-beta production / positive regulation of interleukin-8 production / positive regulation of JNK cascade / microglial cell activation / response to virus / defense response / cellular response to virus / cellular response to type II interferon / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to mechanical stimulus / male gonad development / positive regulation of angiogenesis / MAPK cascade / positive regulation of type II interferon production / transmembrane signaling receptor activity / cellular response to xenobiotic stimulus / positive regulation of tumor necrosis factor production / double-stranded RNA binding / signaling receptor activity / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / early endosome / endosome membrane / inflammatory response / positive regulation of apoptotic process / innate immune response / endoplasmic reticulum membrane / positive regulation of gene expression / cell surface / positive regulation of transcription by RNA polymerase II / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Mus musculus (house mouse) synthetic construct (others) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||
Authors | Sakaniwa, K. / Ohto, U. / Shimizu, T. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Nat Commun / Year: 2023 Title: TLR3 forms a laterally aligned multimeric complex along double-stranded RNA for efficient signal transduction. Authors: Kentaro Sakaniwa / Akiko Fujimura / Takuma Shibata / Hideki Shigematsu / Toru Ekimoto / Masaki Yamamoto / Mitsunori Ikeguchi / Kensuke Miyake / Umeharu Ohto / Toshiyuki Shimizu / Abstract: Toll-like receptor 3 (TLR3) is a member of the TLR family, which plays an important role in the innate immune system and is responsible for recognizing viral double-stranded RNA (dsRNA). Previous ...Toll-like receptor 3 (TLR3) is a member of the TLR family, which plays an important role in the innate immune system and is responsible for recognizing viral double-stranded RNA (dsRNA). Previous biochemical and structural studies have revealed that a minimum length of approximately 40-50 base pairs of dsRNA is necessary for TLR3 binding and dimerization. However, efficient TLR3 activation requires longer dsRNA and the molecular mechanism underlying its dsRNA length-dependent activation remains unknown. Here, we report cryo-electron microscopy analyses of TLR3 complexed with longer dsRNA. TLR3 dimers laterally form a higher multimeric complex along dsRNA, providing the basis for cooperative binding and efficient signal transduction. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wm4.cif.gz | 559.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wm4.ent.gz | 462.6 KB | Display | PDB format |
PDBx/mmJSON format | 7wm4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/7wm4 ftp://data.pdbj.org/pub/pdb/validation_reports/wm/7wm4 | HTTPS FTP |
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-Related structure data
Related structure data | 32599MC 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
-Protein , 1 types, 4 molecules CDEF
#1: Protein | Mass: 77365.852 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tlr3 / Production host: Homo sapiens (human) / References: UniProt: Q99MB1 |
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-RNA chain , 2 types, 2 molecules AB
#2: RNA chain | Mass: 25699.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: RNA chain | Mass: 25676.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Sugars , 3 types, 40 molecules
#4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / |
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-Details
Has ligand of interest | N |
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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: Tetrameric TLR3 in complex with dsRNA (90 bp) / Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: Mus musculus (house mouse) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 5.3 / Details: 25 mM MES-NaOH pH 5.3, 0.3 M NaCl |
Specimen | Conc.: 0.2 mg/ml / Embedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
EM embedding | Material: ice |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 300 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2400 nm / Nominal defocus min: 1400 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 274002 / Symmetry type: POINT | ||||||||||||||||||||||||
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