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- EMDB-30626: 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: EMDB / ID: EMD-30626 | |||||||||
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Title | Mouse Toll-like receptor 3 ectodomain in complex with lncRNA Rmrp in lapped form | |||||||||
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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 / cellular response to exogenous dsRNA / 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 / cellular response to virus / cellular response to type II interferon / defense response / cellular response to mechanical stimulus / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of interleukin-6 production / positive regulation of angiogenesis / positive regulation of type II interferon production / transmembrane signaling receptor activity / male gonad development / MAPK cascade / positive regulation of tumor necrosis factor production / 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 | single particle reconstruction / cryo EM / Resolution: 3.64 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 | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 204.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.3 KB 16.3 KB | Display Display | ![]() |
Images | ![]() | 42.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7dasMC ![]() 7da7C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Cryo-EM structure of mouse Toll-like receptor 3 ectodomain with C...
Entire | Name: Cryo-EM structure of mouse Toll-like receptor 3 ectodomain with C-domain of lncRNA Rmrp |
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Components |
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-Supramolecule #1: Cryo-EM structure of mouse Toll-like receptor 3 ectodomain with C...
Supramolecule | Name: Cryo-EM structure of mouse Toll-like receptor 3 ectodomain with C-domain of lncRNA Rmrp type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Molecular weight | Experimental: 230 KDa |
-Supramolecule #2: Toll-like receptor 3
Supramolecule | Name: Toll-like receptor 3 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() |
-Supramolecule #3: RNA component of mitochondrial RNAase P (Rmrp), RNase MRP RNA
Supramolecule | Name: RNA component of mitochondrial RNAase P (Rmrp), RNase MRP RNA type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Toll-like receptor 3
Macromolecule | Name: Toll-like receptor 3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 78.101648 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: HHHHHHENLY FQSQCTVRYN VADCSHLKLT HIPDDLPSNI TVLNLTHNQL RRLPPTNFTR YSQLAILDAG FNSISKLEPE LCQILPLLK VLNLQHNELS QISDQTFVFC TNLTELDLMS NSIHKIKSNP FKNQKNLIKL DLSHNGLSST KLGTGVQLEN L QELLLAKN ...String: HHHHHHENLY FQSQCTVRYN VADCSHLKLT HIPDDLPSNI TVLNLTHNQL RRLPPTNFTR YSQLAILDAG FNSISKLEPE LCQILPLLK VLNLQHNELS QISDQTFVFC TNLTELDLMS NSIHKIKSNP FKNQKNLIKL DLSHNGLSST KLGTGVQLEN L QELLLAKN KILALRSEEL EFLGNSSLRK LDLSSNPLKE FSPGCFQTIG KLFALLLNNA QLNPHLTEKL CWELSNTSIQ NL SLANNQL LATSESTFSG LKWTNLTQLD LSYNNLHDVG NGSFSYLPSL RYLSLEYNNI QRLSPRSFYG LSNLRYLSLK RAF TKQSVS LASHPNIDDF SFQWLKYLEY LNMDDNNIPS TKSNTFTGLV SLKYLSLSKT FTSLQTLTNE TFVSLAHSPL LTLN LTKNH ISKIANGTFS WLGQLRILDL GLNEIEQKLS GQEWRGLRNI FEIYLSYNKY LQLSTSSFAL VPSLQRLMLR RVALK NVDI SPSPFRPLRN LTILDLSNNN IANINEDLLE GLENLEILDF QHNNLARLWK RANPGGPVNF LKGLSHLHIL NLESNG LDE IPVGVFKNLF ELKSINLGLN NLNKLEPFIF DDQTSLRSLN LQKNLITSVE KDVFGPPFQN LNSLDMRFNP FDCTCES IS WFVNWINQTH TNISELSTHY LCNTPHHYYG FPLKLFDTSS CK |
-Macromolecule #2: RNA component of mitochondrial RNAase P (Rmrp), RNase MRP RNA
Macromolecule | Name: RNA component of mitochondrial RNAase P (Rmrp), RNase MRP RNA type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 48.12452 KDa |
Sequence | String: GCUCGCUCUG AAGGCCUGUU UCCUAGGCUA CAUACGAGGG ACAUGUUCCU UAUCCUUUCG CCUAGGGGAA AGUCCCCGGA AGCUCACAU AGUGACGCAG GCAGUGCGAC CUGGCUCGCA CCAACCACAC GGGGCUCAUU CUCAGCGCGG C |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.0 mg/mL |
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Buffer | pH: 6 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 101.325 kPa |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV |
Details | This sample was mono disperse. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 78.5 K / Max: 78.5 K |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 40 eV |
Details | Preliminary grid screening was preformed manually. |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Number grids imaged: 2 / Number real images: 10617 / Average exposure time: 5.0 sec. / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated defocus max: 2.0 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |