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- PDB-7da7: Mouse Toll-like receptor 3 ectodomain in complex with lncRNA Rmrp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7da7 | ||||||
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Title | Mouse Toll-like receptor 3 ectodomain in complex with lncRNA Rmrp in elongated form | ||||||
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![]() | RNA BINDING PROTEIN/RNA / complex / innate immune system / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | ![]() 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 type I interferon production / positive regulation of interferon-alpha production / cellular response to interferon-beta / extrinsic apoptotic signaling pathway / positive regulation of chemokine production / 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 / cellular response to virus / defense response / cellular response to type II interferon / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to mechanical stimulus / positive regulation of angiogenesis / transmembrane signaling receptor activity / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / male gonad development / positive regulation of type II interferon production / MAPK cascade / double-stranded RNA binding / cellular response to xenobiotic stimulus / signaling receptor activity / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / early endosome / endosome membrane / inflammatory response / positive regulation of apoptotic process / innate immune response / endoplasmic reticulum membrane / cell surface / positive regulation of transcription by RNA polymerase II / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.47 Å | ||||||
![]() | Li, B. / Cao, X. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Endosomal lncRNA Rmrp is required for TLR3 innate sensing by engaging TLR3 dimerization Authors: Zhang, S. / Li, B. / Cao, X. | ||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 266.5 KB | Display | ![]() |
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PDB format | ![]() | 217.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 783.8 KB | Display | ![]() |
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Full document | ![]() | 810.2 KB | Display | |
Data in XML | ![]() | 43.6 KB | Display | |
Data in CIF | ![]() | 67.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 30624MC ![]() 7dasC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 78101.648 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: RNA chain | | Mass: 48124.520 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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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: Cryo-EM structure of mouse Toll-like receptor 3 ectodomain with C-domain of lncRNA Rmrp Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 0.23 MDa / Experimental value: YES |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 6 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was mono disperse. |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K |
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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 / Details: Preliminary grid screening was preformed manually. |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 2000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 78.5 K / Temperature (min): 78.5 K |
Image recording | Average exposure time: 5 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 10617 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 40 eV |
Image scans | Movie frames/image: 40 |
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Processing
EM software |
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Image processing | Details: The selected images were normalized. | ||||||||||||||||||||||||||||||||||||
CTF correction | Details: CTF correction was done by patch CTF correction. / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2545278 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 108128 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 97.5 / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 3CIG Pdb chain-ID: A / Pdb chain residue range: 27-697 |